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Sample records for 3d velocity structure

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  3. Analysis of the rupture process of the 1995 Kobe earthquake using a 3D velocity structure

    NASA Astrophysics Data System (ADS)

    Guo, Yujia; Koketsu, Kazuki; Ohno, Taichi

    2013-12-01

    A notable feature of the 1995 Kobe (Hyogo-ken Nanbu) earthquake is that violent ground motions occurred in a narrow zone. Previous studies have shown that the origin of such motions can be explained by the 3D velocity structure in this zone. This indicates not only that the 3D velocity structure significantly affects strong ground motions, but also that we should consider its effects in order to determine accurately the rupture process of the earthquake. Therefore, we have performed a joint source inversion of strong-motion, geodetic, and teleseismic data, where 3D Green's functions were calculated for strong-motion and geodetic data in the Osaka basin. Our source model estimates the total seismic moment to be about 2.1 × 1019 N m and the maximum slip reaches 2.9 m near the hypocenter. Although the locations of large slips are similar to those reported by Yoshida et al. (1996), there are quantitative differences between our results and their results due to the differences between the 3D and 1D Green's functions. We have also confirmed that our source model realized a better fit to the strong motion observations, and a similar fit as Yoshida et al. (1996) to the observed static displacements.

  4. 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

  5. 3D velocity structure of upper crust beneath NW Bohemia/Vogtland

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    The 3D structure of the upper crust beneath west Bohemia/Vogtland region, analyzed with travel time tomography and ambient noise surface wave tomography using existing data. This region is characterized by a series of phenomena like occurrence of repeated earthquake swarms, surface exhalation, CO2 enriched fluids, mofettes, mineral springs and enhanced heat flow, and has been proposed as an excellent location for an ICDP drilling project targeted to a better understanding of the crust in an active magmatic environment. We performed a 3D tomography using P-and S-wave travel times of local earthquakes and explosions. The data set were taken from permanent and temporary seismic networks in Germany and Czech Republic from 2000 to 2010, as well as active seismic experiments like Celebration 2000 and quarry blasts. After picking P and S wave arrival times, 399 events which were recorded by 9 or more stations and azimuthal gap<160° were selected for inversion. A simultaneous inversion of P and S wave 1D velocity models together with relocations of hypocenters and station corrections was performed. The obtained minimum 1D velocity model was used as starting model for the 3D Vp and Vp/Vs velocity models. P and S wave travel time tomography employs damped least-square method and ray tracing by pseudo-bending algorithm. For model parametrization different cell node spacings have been tested to evaluate the resolution in each node. Synthetic checkerboard tests have been done to check the structural resolution. Then Vp and Vp/Vs in the preferred 3D grid model have been determined. Earthquakes locations in iteration process change till the hypocenter adjustments and travel time residuals become smaller than the defined threshold criteria. Finally the analysis of the resolution depicts the well resolved features for interpretation. We observed lower Vp/Vs ratio in depth of 5-10 km close to the foci of earthquake swarms and higher Vp/Vs ratio is observed in Saxoturingian zone and

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

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  9. 3-D Crustal Velocity Structure Across the Vrancea Zone in Romania, Derived From Seismic Data

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

  10. 3-D Isotropic and Anisotropic S-velocity Structure in the North American Upper Mantle

    NASA Astrophysics Data System (ADS)

    Yuan, H.; Marone, F.; Romanowicz, B.; Abt, D.; Fischer, K.

    2008-12-01

    The tectonic diversity of the North American continent has led to a number of geological, tectonic and geodynamical models, many of which can be better tested with high resolution 3-d tomographic models of the isotropic and anisotropic mantle structure of the continent. In the framework of non-linear asymptotic coupling theory (NACT), we recently developed tools to invert long period seismic waveforms combined with SKS splitting data, for both isotropic and radial and azimuthal anisotropic S-wave velocity structure in the upper mantle at the continental scale (Marone et al., 2007; Marone and Romanowicz, 2007). Striking differences in both isotropic and anisotropic velocity structure were observed: beneath the high velocity stable cratonic region a distinct two-layer anisotropic domain is present, with the bottom layer fast axis direction aligned with the absolute plate motion, and a shallower lithospheric layer with north pointing fast axis most likely showing records of past tectonic history; under the active western US the direction of tomographically inferred anisotropy is stable with depth and compatible with the absolute plate motion direction. Here we present an updated model which includes nearly five more years of data, including data from newly operative USArray stations, and a somewhat more extended frequency band. Our new model confirms our previous results, and reveals greater yet complex details of the anisotropic velocity structure beneath the western U.S.. We also show initial results of incorporating constraints on the depth to the lithosphere-asthenosphere boundary (LAB) using teleseismic receiver functions. We discuss the different anisotropic domains resolved both laterally and in depth, in the context of tectonic history of the north American continent.

  11. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    SciTech Connect

    Lestari, Titik; Nugraha, Andri Dian

    2015-04-24

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA’s) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 – April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

  12. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    NASA Astrophysics Data System (ADS)

    Lestari, Titik; Nugraha, Andri Dian

    2015-04-01

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA's) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 - April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  14. 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

  15. 3D P-Wave Velocity Structure of the Deep Galicia Rifted Margin

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy; Davy, Richard; Sawyer, Dale; Klaeschen, Dirk; Papenberg, Cord; Reston, Timothy; Shillington, Donna; Ranero, Cesar

    2015-04-01

    The combined wide-angle reflection-refraction and multi-channel seismic (MCS) experiment, Galicia 3D, was carried out in 2013 at the Galicia rifted margin in the northeast Atlantic Ocean, west of Spain. The main geological features within the 64 by 20 km (1280 km²) 3D box investigated by the survey are the peridotite ridge (PR), the fault bounded, rotated basement blocks and the S reflector, which has been interpreted to be a low angle detachment fault. 44 short period four-component ocean bottom seismometers and 28 ocean bottom hydrophones were deployed in the 3D box. 3D MCS profiles sampling the whole box were acquired with two airgun arrays of 3300 cu.in. fired alternately every 37.5 m. We present the results from 3D first-arrival time tomography that constrains the P-wave velocity in the 3D box, for the entire depth sampled by reflection data. Results are validated by synthetic tests and by the comparison with Galicia 3D MCS lines. The main outcomes are as follows: 1- The 3.5 km/s iso-velocity contour mimics the top of the acoustic basement observed on MCS profiles. Block bounding faults are imaged as velocity contrasts and basement blocks exhibit 3D topographic variations. 2- On the southern profiles, the top of the PR rises up to 5.5 km depth whereas, 20 km northward, its basement expression (at 6.5 km depth) nearly disappears. 3- The 6.5 km/s iso-velocity contour matches the topography of the S reflector where the latter is visible on MCS profiles. Within a depth interval of 0.6 km (in average), velocities beneath the S reflector increase from 6.5 km/s to 7 km/s, which would correspond to a decrease in the degree of serpentinization from ~45 % to ~30 % if these velocity variations are caused solely by variations in hydration. At the intersections between the block bounding normal faults and the S reflector, this decrease happens over a larger depth interval (> 1 km), suggesting that faults act as conduit for the water flow in the upper mantle.

  16. 3-D P Wave Velocity Structure of Marmara Region Using Local Earthquake Tomography

    NASA Astrophysics Data System (ADS)

    Işık, S. E.; Gurbuz, C.

    2014-12-01

    The 3D P wave velocity model of upper and lower crust of the Marmara Region between 40.200- 41.200N and 26.500- 30.500E is obtained by tomographic inversion (Simulps) of 47034 P wave arrivals of local earthquakes recorded at 90 land stations between October 2009 and December 2012 and 30 OBO stations and 14162 shot arrivals recorded at 35 OBO stations (Seismarmara Survey, 2001). We first obtained a 1D minimum model with Velest code in order to obtain an initial model for 3D inversion with 648 well located earthquakes located within the study area. After several 3D inversion trials we decided to create a more adequate initial model for 3D inversion. Choosing the initial model we estimated the 3D P wave velocity model representing the whole region both for land and sea. The results are tested by making Checkerboard , Restoring Resolution and Characteristic Tests, and the reliable areas of the resulting model is defined in terms of RDE, DWS, SF and Hit count distributions. By taking cross sections from the resulting model we observed the vertical velocity change along profiles crossing both land and sea. All the profiles crossing the basins showed that the high velocities of lower crust make extensions towards the basin area which looks like the force that gives a shape to the basins. These extensions of lower crust towards the basins appeared with an average velocity of 6.3 km/s which might be the result of the deformation due the shearing in the region. It is also interpreted that the development of these high velocities coincide with the development of the basins. Thus, both the basins and the high velocity zones around them might be resulted from the entrance of the NAF into the Marmara Sea and at the same time a shear regime was dominated due to the resistance of the northern Marmara Region (Yılmaz, 2010). The seismicity is observed between 5 km and 15 km after the 3D location of the earthquakes. The locations of the earthquakes improved and the seismogenic zone

  17. 3D Seismic Velocity Structure Around Philippine Sea Slab Subducting Beneath Kii Peninsula, Japan

    NASA Astrophysics Data System (ADS)

    Shibutani, T.; Imai, M.; Hirahara, K.; Nakao, S.

    2013-12-01

    Kii Peninsula is a part of the source area of Nankai Trough megaquakes and the region through which the strong seismic waves propagate to big cities in Kansai such as Osaka, Kyoto, Nara, Kobe, and so on. Moreover, the rupture starting point is thought to be possibly at off the peninsula. Therefore, it is important for simulations of the megaquakes and the strong motions to estimate accurately the configuration of the Philippine Sea slab and the seismic velocity structure around the slab and to investigate properties and conditions of the plate boundary surface. Deep low frequency events (DLFEs) are widely distributed from western Shikoku to central Tokai at 30 - 40 km depths on the plate boundary (Obara, 2002). Results from seismic tomography and receiver function analyses revealed that the oceanic crust of the Philippine Sea plate had a low velocity and a high Vp/Vs ratio (Hirose et al., 2007; Ueno et al., 2008). Hot springs with high 3He/4He ratios are found in an area between central Kinki and Kii Peninsula despite in the forearc region (Sano and Wakita, 1985). These phenomena suggest the process that H2O subducting with the oceanic crust dehydrates at the depths, causes the DLFEs, and moves to shallower depths. We carried out linear array seismic observations in the Kii Peninsula since 2004 in order to estimate the structure of the Philippine Sea slab and the surrounding area. We have performed receiver function analyses for four profile lines in the dipping direction of the slab and two lines in the perpendicular direction so far. We estimated three dimensional shapes of seismic velocity discontinuities such as the continental Moho, the upper surface of the oceanic crust and the oceanic Moho (Imai et al., 2013, this session). In addition, we performed seismic tomography with a velocity model embedded the discontinuities and observed travel times at stations in the linear arrays, and successfully estimated 3D seismic velocity structure around the Philippine Sea

  18. Comparative velocity structure of active Hawaiian volcanoes from 3-D onshore-offshore seismic tomography

    USGS Publications Warehouse

    Park, J.; Morgan, J.K.; Zelt, C.A.; Okubo, P.G.; Peters, L.; Benesh, N.

    2007-01-01

    We present a 3-D P-wave velocity model of the combined subaerial and submarine portions of the southeastern part of the Island of Hawaii, based on first-arrival seismic tomography of marine airgun shots recorded by the onland seismic network. Our model shows that high-velocity materials (6.5-7.0??km/s) lie beneath Kilauea's summit, Koae fault zone, and the upper Southwest Rift Zone (SWRZ) and upper and middle East Rift Zone (ERZ), indicative of magma cumulates within the volcanic edifice. A separate high-velocity body of 6.5-6.9??km/s within Kilauea's lower ERZ and upper Puna Ridge suggests a distinct body of magma cumulates, possibly connected to the summit magma cumulates at depth. The two cumulate bodies within Kilauea's ERZ may have undergone separate ductile flow seaward, influencing the submarine morphology of Kilauea's south flank. Low velocities (5.0-6.3??km/s) seaward of Kilauea's Hilina fault zone, and along Mauna Loa's seaward facing Kao'iki fault zone, are attributed to thick piles of volcaniclastic sediments deposited on the submarine flanks. Loihi seamount shows high-velocity anomalies beneath the summit and along the rift zones, similar to the interpreted magma cumulates below Mauna Loa and Kilauea volcanoes, and a low-velocity anomaly beneath the oceanic crust, probably indicative of melt within the upper mantle. Around Kilauea's submarine flank, a high-velocity anomaly beneath the outer bench suggests the presence of an ancient seamount that may obstruct outward spreading of the flank. Mauna Loa's southeast flank is also marked by a large, anomalously high-velocity feature (7.0-7.4??km/s), interpreted to define an inactive, buried volcanic rift zone, which might provide a new explanation for the westward migration of Mauna Loa's current SWRZ and the growth of Kilauea's SWRZ. ?? 2007 Elsevier B.V. All rights reserved.

  19. 3-D Velocity Structure of Southwestern British Columbia and Northern Washington

    NASA Astrophysics Data System (ADS)

    Ramachandran, K.; Ramachandran, K.; Spence, G. D.; Dosso, S.; Hyndman, R. D.; Hyndman, R. D.; Brocher, T. M.; Fisher, M. M.

    2001-12-01

    A seismic tomography analysis in S.W. British Columbia and N. Washington has been used to define the velocity structure of the forearc crust and underlying subducting Juan de Fuca plate, and to obtain precise earthquake locations. First arrival travel-times from earthquakes and from the large airgun array used in the `Seismic Hazards Investigation of Puget Sound' (SHIPS) 1998 experiment, were simultaneously inverted for hypocentral parameters and velocity structure. Approximately 16,000 picks from 1,400 earthquakes recorded at 46 permanent stations, and 35,000 picks from the SHIPS experiment were used in the inversion. The velocity model was parameterized in the forward/inverse step by a node/cell spacing of 3 X 3 X 3 km over a volume of 360 X 450 X 93 km depth. The starting and final RMS travel time misfits were 479 ms and 120 ms respectively. Checkerboard tests conducted on the final velocity model imply good lateral resolution ranging from 30 to 50 km. The SHIPS airgun data mainly constrained the upper ~12 km and the earthquake data the deeper structure. The high velocity mafic Crescent Terrane that dips beneath the margin is well mapped in the velocity model on a regional scale. Its thickness beneath southern Vancouver Island is interpreted to reach ~20 km. Three high velocity structures above the subducting Juan de Fuca plate, having mafic to ultramafic velocities of 7.25-7.5 km/s, occur beneath southern Vancouver Island and Puget Sound at a depth of ~25 km. They may be associated with deeper parts of the Crescent Terrane, or with structures such as seamounts on the subducting Juan de Fuca plate. At the southern tip of Vancouver Islands, the Leech River Fault, Southern Whidbey Island Fault, and the Devils Mountain Fault appear to correlate with mapped seismicity. The subducting Juan de Fuca plate is well mapped beneath southern Vancouver Island, Olympic Peninsula, Strait of Georgia, and Puget Sound. The velocity model identifies the steepening dip in the

  20. 3D P-Wave Velocity Structure of the Crust and Relocation of Earthquakes in 21 the Lushan Source Area

    NASA Astrophysics Data System (ADS)

    Yu, X.; Wang, X.; Zhang, W.

    2014-12-01

    The double difference seismic tomography method is applied to the absolute first arrival P wave arrival times and high quality relative P arrival times of the Lushan seismic sequence to determine the detailed crustal 3D P wave velocity structure and the hypocenter parameters in the Lushan seismic area. The results show that the Lushan mainshock locates at 30.28 N, 103.98 E, with the depth of 16.38 km. The leading edge of aftershock in the northeast of mainshock present a spade with a steep dip angle, the aftershocks' extended length is about 12 km. In the southwest of the Lushan mainshock, the leading edge of aftershock in low velocity zone slope gently, the aftershocks' extended length is about 23 km. The P wave velocity structure of the Lushan seismic area shows obviously lateral heterogeneity. The P wave velocity anomalies represent close relationship with topographic relief and geological structure. In Baoxing area the complex rocks correspond obvious high-velocity anomalies extending down to 15 km depth,while the Cenozoic rocks are correlated with low-velocity anomalies. Our high-resolution tomographic model not only displays the general features contained in the previous models, but also reveals some new features. An obvious high-velocity anomaly is visible in Daxing area. The high-velocity anomalies beneath Baoxing and Daxing connect each other in 10 km depth, which makes the contrast between high and low velocity anomalies more sharp. Above 20 km depth the velocity structure in southwest and northeast segment of the mainshock shows a big difference: low-velocity anomalies are dominated the southwest segment, while high-velocity anomalies rule the northeast segment. The Lushan mainshock locates at the leading edge of a low-velocity anomaly surrounded by the Baoxing and Daxing high-velocity anomalies. The Lushan aftershocks in southwest are distributed in low-velocity anomalies or the transition belt: the footwall represents low-velocity anomalies, while

  1. On the Velocity Field and the 3D Structure of the Galactic Soccer Ball Abell 43

    NASA Astrophysics Data System (ADS)

    Rauch, Thomas; Werner, Klaus; Ercolano, Barbara; Köppen, Joachim

    2005-11-01

    Planetary nebulae (PNe) and their central stars (CSs) are ideal tools to test evolutionary theory: photospheric properties of their exciting stars give stringent constraints for theoretical predictions of stellar evolution. The nebular abundances display the star's photosphere chemical composition at the time of the nebula's ejection which allows to look back into the history of stellar evolution. More importantly, they even provide a possibility to investigate on the chemical evolution of our Galaxy because most of the nuclear processed material goes back into the interstellar medium via PNe. The recent developments in observation techniques and the new three-dimensional photoionization code MOCASSIN (Ercolano et al. 2003) enable us to analyze PNe properties accurately by the construction of consistent models of PNe and CSs. In addition to PNe imaging and spectroscopy, detailed information about the velocity field within the PNe is a pre-requisite to employ de-projection techniques in modeling the physical structure of the PNe.

  2. 3D P-wave velocity structure of the crust and relocation of earthquakes in the Lushan, China, source area

    NASA Astrophysics Data System (ADS)

    Yu, Xiangwei; Wang, Xiaona; Zhang, Wenbo

    2016-04-01

    Many researchers have investigated the Lushan source area with geological and geophysical approaches since the 2013 Lushan, China, earthquake happened. Compared with the previous tomographic studies, we have used a much large data set and an updated tomographic method to determine a small scale three-dimensional P wave velocity structure with spatial resolution less than 5km, which plays the important role for understanding the deep structure and the genetic mechanism beneath the Lushan area. The double difference seismic tomography method is applied to 50,711 absolute first arrival P wave arrival times and 7,294,691 high quality relative P arrival times of 5,285 events of Lushan seismic sequence to simultaneously determine the detailed crustal 3D P wave velocity structure and the hypocenter parameters in the Lushan seismic area. This method takes account of the path anomaly biases explicitly by making full use of valuable information of seismic wave propagation jointly with absolute and relative arrival time data. Our results show that the Lushan mainshock locates at 30.28N, 103.98E, with the depth of 16.38km. The front edge of aftershock in the northeast of mainshock present a spade with a steep dip angle, the aftershocks' extended length is about 12km. In the southwest of Lushan mainshock, the front edge of aftershock in low velocity zone slope gently, the aftershocks' extended length is about 23km. Our high-resolution tomographic model not only displays the general features contained in the previous models, but also reveals some new features. The Tianquan, Shuangshi and Daguan line lies in the transition zone between high velocity anomalies to the southeast and low velocity anomalies to the northwest at the ground surface. An obvious high-velocity anomaly is visible in Daxing area. With the depth increasing, Baoxing high velocity anomaly extends to Lingguan, while the southeast of the Tianquan, Shuangshi and Daguan line still shows low velocity. The high-velocity

  3. Numerical Modeling of seismic wave propagation on Etna Volcano (Italy): Construction of 3D realistic velocity structures

    NASA Astrophysics Data System (ADS)

    Trovato, Claudio; Aochi, Hideo; De Martin, Florent

    2014-05-01

    Understanding the source mechanism of long-period (LP) seismic signals on volcanoes is an important key point in volcanology and for the hazard forecasting. In the last decades, moment tensor inversions have led to various descriptions of the kinematic source mechanism. These inversions suppose a relatively simple structure of the medium. However, the seismic wave propagation in a realistic 3-D volcano model should be taken into account for understanding the complicated physical processes of magma and gas behaviors at depth. We are studying Etna volcano, Italy, to understand the volcanic processes during different stages of activity. We adopt a spectral element method (SEM), a code EFISPEC3D (De Martin, BSSA, 2011), which shows a good accuracy and numerical stability in the simulations of seismic wave propagation. First we construct the geometrical model. We use a digital elevation model (DEM) to generate finite element meshes with a spacing of 50 m on the ground surface. We aim to calculate the ground motions until 3 Hz for the shallowest layer with Vs = ~500 m/s. The minimal size of the hexahedral elements is required to be around 100 m, with a total number of elements n = ~2 10 ^ 6 for the whole model. We compare different velocity structure configurations. We start with a homogeneous medium and add complexities taking in account the shallow low velocity structure. We also introduce a velocity gradient towards depth. Simulations performed in the homogeneous medium turn in approximately 20 hours for calculations parallelized on 16 CPUs. Complex velocity models should take approximately the same time of computation. We then try to simulate the ground motion from the LP sources (0.1-1.5 Hz) obtained by the inversion for the Etna volcano in 2008 (De Barros, GRL, 2009 and De Barros, JGR, 2011). Some vertical and horizontal structures can be added to reproduce injected dikes or sills respectively.

  4. 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.

  5. 3-D velocity structure around tehri region of the garhwal lesser himalaya: constraints on geometry of the underthrusting indian plate

    NASA Astrophysics Data System (ADS)

    Kanaujia, Jyotima; Kumar, Ashwani; Gupta, S. C.

    2016-02-01

    We investigate the upper crustal velocity structure beneath the Tehri region of the Garhwal Himalaya. The investigated region is situated within the 700-km-long central seismic gap of the Himalaya that has experienced three gap-filling earthquakes since 1991 including the recent 2015 Nepal earthquake (Mw 7.8). The local tomographic inversion is based on a dataset of 1365 events collected from January 2008 to December 2012 by a 12-station local network that covers an area of about 100 × 80 km around Tehri Dam. We perform a simultaneous inversion for P- and S-wave velocity anomalies. Tomograms are interpreted in the backdrop of the regional geological and tectonic framework of the region. The spatial distribution of relocated events from the 3- D velocity model has shed new light on the pattern of seismicity in the vicinity of the Main Central thrust (MCT), and has elucidated the structure of the underthrusting Indian plate. Our model exhibits a significant negative velocity anomaly up to ˜5 per cent beneath the central part of the Garhwal Inner Lesser Himalaya, and a P-wave low velocity anomaly near the Chamoli region. The seismicity zone around the Chamoli region may be attributed to the presence of fluid filled rocks. Furthermore, an area with˜3-4 per cent positive velocity anomaly is delineated to the northwest of the Uttarkashi thrust in the vicinity of the MCT. Significant findings of the study include: a flat-ramp-flat type sub-surface geometry of the underthrusting Indian plate below the Garhwal Himalaya, high velocity images representing the trend and configuration of Delhi-Haridwar-ridge below the Sub Himalaya and Lesser Himalaya, and a seismically active zone representing geometrical asperity on the basement thrust in the vicinity of the MCT.

  6. Azimuthally Anisotropic 3D Velocity Continuation

    DOE PAGESBeta

    Burnett, William; Fomel, Sergey

    2011-01-01

    We extend time-domain velocity continuation to the zero-offset 3D azimuthally anisotropic case. Velocity continuation describes how a seismic image changes given a change in migration velocity. This description turns out to be of a wave propagation process, in which images change along a velocity axis. In the anisotropic case, the velocity model is multiparameter. Therefore, anisotropic image propagation is multidimensional. We use a three-parameter slowness model, which is related to azimuthal variations in velocity, as well as their principal directions. This information is useful for fracture and reservoir characterization from seismic data. We provide synthetic diffraction imaging examples to illustratemore » the concept and potential applications of azimuthal velocity continuation and to analyze the impulse response of the 3D velocity continuation operator.« less

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  8. 3-D velocity structures, seismicity patterns, and their tectonic implications across the Andean Foreland of San Juan Argentina

    NASA Astrophysics Data System (ADS)

    Asmerom, Biniam Beyene

    Three-dimensional velocity structures and seismicity patterns have been studied across the Andean Foreland of San Juan Argentina using data acquired by PANDA deployment. Distinct velocity variations are revealed between Precordillera in the west and Pie de Palo in the east. The low velocity anomaly beneath Precordillera is associated with the presence of thick sedimentary rocks and thick sediment cover of Matagusanos valley. Similarly, the high velocity anomaly east of Eastern Precordillera is correlated with the presence of basement rocks. These anomalies are observed from the station corrections of Joint Hypocentral Determination (JHD) analysis. A northeast trending west dipping high velocity anomaly is imaged beneath the southern half of Pie de Palo. This anomaly represents a Grenvillian suture zone formed when Pie de Palo collided with the Precordillera. Relocated seismicity using 3-D Vp and Vs models obtained in this study revealed crustal scale buried faults beneath the Eastern Precordillera and Sierra Pie de Palo. The fault defined by the seismicity extend down to a depth of ˜ 40 km and ~35 km beneath Precordillera and Pie de Palo, respectively, defining the lower bound of the brittle to ductile transition of the crust. These results confirm that present day active crustal thickening involves the entire crust in the tectonic process and results in thick-skinned deformation beneath both the Eastern Precordillera and Pie de Palo. Based on the seismicity pattern, geomorphology, and velocity structures, Sierra Pie de Palo, a basement uplift block, can be divided into two separate semi-blocks separated by a northeast trending fracture zone. The northern block is characterized by a well-defined west dipping fault and low Vp/Vs ratio particularly at a depth of 12 to 16 km, while the southern block shows a poorly-defined east dipping fault with high Vp/Vs ratio at a depth of 20 to 26 km. Spatial distribution of the well-relocated crustal earthquakes along these

  9. Modeling and validation of a 3D velocity structure for the Santa Clara Valley, California, for seismic-wave simulations

    USGS Publications Warehouse

    Hartzell, S.; Harmsen, S.; Williams, R.A.; Carver, D.; Frankel, A.; Choy, G.; Liu, P.-C.; Jachens, R.C.; Brocher, T.M.; Wentworth, C.M.

    2006-01-01

    A 3D seismic velocity and attenuation model is developed for Santa Clara Valley, California, and its surrounding uplands to predict ground motions from scenario earthquakes. The model is developed using a variety of geologic and geophysical data. Our starting point is a 3D geologic model developed primarily from geologic mapping and gravity and magnetic surveys. An initial velocity model is constructed by using seismic velocities from boreholes, reflection/refraction lines, and spatial autocorrelation microtremor surveys. This model is further refined and the seismic attenuation is estimated through waveform modeling of weak motions from small local events and strong-ground motion from the 1989 Loma Prieta earthquake. Waveforms are calculated to an upper frequency of 1 Hz using a parallelized finite-difference code that utilizes two regions with a factor of 3 difference in grid spacing to reduce memory requirements. Cenozoic basins trap and strongly amplify ground motions. This effect is particularly strong in the Evergreen Basin on the northeastern side of the Santa Clara Valley, where the steeply dipping Silver Creek fault forms the southwestern boundary of the basin. In comparison, the Cupertino Basin on the southwestern side of the valley has a more moderate response, which is attributed to a greater age and velocity of the Cenozoic fill. Surface waves play a major role in the ground motion of sedimentary basins, and they are seen to strongly develop along the western margins of the Santa Clara Valley for our simulation of the Loma Prieta earthquake.

  10. 3D Seismic Velocity Structure in the Rupture Area of the 2010 Maule Mw=8.8 Earthquake

    NASA Astrophysics Data System (ADS)

    Hicks, S. P.; Rietbrock, A.; Ryder, I. M.; Nippress, S.; Haberland, C. A.

    2011-12-01

    The 2010 Mw=8.8 Maule, Chile earthquake is one of the largest subduction zone earthquakes ever recorded. Up to now numerous co-seismic and some post-seismic slip models have been published based entirely on seismological, geodetic, or tsunami run-up heights, or combinations of these data. Most of these models use a simplified megathrust geometry derived mainly from global earthquake catalogues, and also simplified models of seismic parameters (e.g. shear modulus). By using arrival times for a vast number of aftershocks that have been recorded on a temporary seismic array, we present a new model for the slab geometry based on earthquake locations together with a new 3D seismic velocity model of the region, for both vp and vp/vs. We analyzed 3552 aftershocks that occurred between 18 March and 24 May 2011, recorded by the International Maule Aftershock Dataset (IMAD) seismic network. Event selection from a catalogue of automatically-determined events was based on 20 or more arrival times, from which at least 10 are S-wave observations. In total over 170,000 arrival times (~125,000 and 45,000 P and S wave arrival times respectively) are used for the tomographic reconstructions. Initially, events were relocated in a 2D velocity model based on a previously published model for the southern end of the rupture area (Haberland et al., 2009). Afterwards a staggered inversion scheme is implemented, starting with a 2D inversion followed by a coarse 3D and a subsequent fine 3D inversion. Based on our preliminary inversions we conclude that aftershock seismicity is mainly concentrated between 20 and 35 km depth along the subduction interface. A second band of seismicity between 40 and 50 km depth is also observed. Low seismic velocities and an increased vp/vs ratio characterize the marine forearc. The obtained velocity model will be discussed.

  11. Segmentation of Hypocenters and 3-D Velocity Structure around the Kii Peninsula Revealed by Onshore and Offshore Seismic Observations

    NASA Astrophysics Data System (ADS)

    Akuhara, T.; Mochizuki, K.; Nakahigashi, K.; Yamada, T.; Shinohara, M.; Sakai, S.; Kanazawa, T.; Uehira, K.; Shimizu, H.

    2013-12-01

    The Philippine Sea Plate subducts beneath the Eurasian Plate at a rate of ~4 cm/year along the Nankai Trough, southwest of Japan. Around the Kii Peninsula, the rupture boundary of the historical Tonankai and Nankai large earthquakes is located, and previous researches have revealed along-strike segmentation of hypocenters [Mochizuki et al., 2010], P-wave anisotropy [Ishise et al., 2009], low frequency earthquake (LFE) distribution [e.g., Obara, 2010] and subduction depth of the Philippine Sea (PHS) Plate, or there may exist a split in the PHS Plate [Ide et al., 2010]. To investigate such segmentation, in our previous work we determined 3-D velocity structure and hypocenters using P- and S-wave arrival times of earthquakes recorded by both ocean bottom seismometers (OBSs) that were deployed from 2003 to 2007 and on-land stations [Akuhara et al., 2013]. As a result, it was discovered that Vp/Vs ratio is also segmented within the oceanic crust and at the bottom of the overriding plate, which coincides with the LFE distribution: segment A is located along the Kii Channel, segment B around the western Kii Peninsula, and segment C around the eastern Kii Peninsula. In segment B, Vp/Vs ratio is low within the oceanic crust and LFE cluster characterized by an anomalously small amount of cumulative slip, compared to the other LFE clusters around the Kii Peninsula, is located [Obara, 2010]. The difference of Vp/Vs ratio and LFE activity among segments were interpreted as difference of pore fluid pressure. In fact, similar segmentation can be seen in hypocenters: Segment A with concentrated seismicity in the oceanic mantle, segment B with that in the oceanic crust, and segment C with little seismicity. To derive characteristic patterns of the hypocenters, we conducted a cluster analysis of earthquakes based on waveform similarity represented by cross-correlation coefficients (CCs) [e.g., Cattaneo, 1999], in which we took varying structural site effects among the OBS stations

  12. 3-D P- and S-wave velocity structure and low-frequency earthquake locations in the Parkfield, California region

    NASA Astrophysics Data System (ADS)

    Zeng, Xiangfang; Thurber, Clifford H.; Shelly, David R.; Harrington, Rebecca M.; Cochran, Elizabeth S.; Bennington, Ninfa L.; Peterson, Dana; Guo, Bin; McClement, Kara

    2016-09-01

    To refine the 3-D seismic velocity model in the greater Parkfield, California region, a new data set including regular earthquakes, shots, quarry blasts and low-frequency earthquakes (LFEs) was assembled. Hundreds of traces of each LFE family at two temporary arrays were stacked with time-frequency domain phase weighted stacking method to improve signal-to-noise ratio. We extend our model resolution to lower crustal depth with LFE data. Our result images not only previously identified features but also low velocity zones (LVZs) in the area around the LFEs and the lower crust beneath the southern Rinconada Fault. The former LVZ is consistent with high fluid pressure that can account for several aspects of LFE behaviour. The latter LVZ is consistent with a high conductivity zone in magnetotelluric studies. A new Vs model was developed with S picks that were obtained with a new autopicker. At shallow depth, the low Vs areas underlie the strongest shaking areas in the 2004 Parkfield earthquake. We relocate LFE families and analyse the location uncertainties with the NonLinLoc and tomoDD codes. The two methods yield similar results.

  13. High resolution 3D P wave velocity structure beneath Tenerife Island (Canary Islands, Spain) based on tomographic inversion of active-source data

    NASA Astrophysics Data System (ADS)

    GarcíA-Yeguas, Araceli; Koulakov, Ivan; IbáñEz, Jesús M.; Rietbrock, A.

    2012-09-01

    We present a high resolution 3 dimensional (3D) P wave velocity model for Tenerife Island, Canaries, covering the top of Teide volcano (3,718 m a.s.l.) down to around 8 km below sea level (b.s.l). The tomographic inversion is based on a large data set of travel times obtained from a 3D active seismic experiment using offshore shots (air guns) recorded at more than 100 onshore seismic stations. The obtained seismic velocity structure is strongly heterogeneous with significant (up to 40%) lateral variations. The main volcanic structure of the Las Cañadas-Teide-Pico Viejo Complex (CTPVC) is characterized by a high P wave velocity body, similar to many other stratovolcanoes. The presence of different high P wave velocity regions inside the CTPVC may be related to the geological and volcanological evolution of the system. The presence of high P wave velocities at the center of the island is interpreted as evidence for a single central volcanic source for the formation of Tenerife. Furthermore, reduced P wave velocities are found in a small confined region in CTPVC and are more likely related to hydrothermal alteration, as indicated by the existence of fumaroles, than to the presence of a magma chamber beneath the system. In the external regions, surrounding CTPVC a few lower P wave velocity regions can be interpreted as fractured zones, hydrothermal alterations, porous materials and thick volcaniclastic deposits.

  14. 2D and 3D Shear-Wave Velocity Structure to >1 Km Depth from Ambient and Active Surface Waves: Three "Deep Remi" Case Studies

    NASA Astrophysics Data System (ADS)

    Louie, J. N.; Pancha, A.; Pullammanappallil, S. K.

    2014-12-01

    Refraction microtermor routinely assesses 1D and 2D velocity-depth profiles to shallow depths of approximately 100 m primarily for engineering applications. Estimation of both shallow and deep (>100 m) shear-velocity structure are key elements in the assessment of urban areas for potential earthquake ground shaking, damage, and the calibration of recorded ground motions. Three independent studies investigated the ability of the refraction microtremor technology to image deep velocity structure, to depths exceeding 1 km (Deep ReMi). In the first study, we were able to delineate basin thicknesses of up to 900 m and the deep-basin velocity structure beneath the Reno-area basin. Constraints on lateral velocity changes in 3D as well as on velocity profiles extended down to 1500 m, and show a possible fault offset. This deployment used 30 stand-alone wireless instruments mated to 4.5 Hz geophones, along each of five arrays 2.9 to 5.8 km long. Rayleigh-wave dispersion was clear at frequencies as low as 0.5 Hz using 120 sec ambient urban noise records. The results allowed construction of a 3D velocity model, vetted by agreement with gravity studies. In a second test, a 5.8 km array delimited the southern edge of the Tahoe Basin, with constraints from gravity. There, bedrock depth increased by 250 m in thickness over a distance of 1600 m, with definition of the velocity of the deeper basin sediments. The third study delineated the collapse region of an underground nuclear explosion within a thick sequence of volcanic extrusives, using a shear-wave minivibe in a radial direction, and horizontal geophones. Analysis showed the cavity extends to 620 m depth, with a width of 180 m and a height of 220 m. Our results demonstrate that deep velocity structure can be recovered using ambient noise. This technique offers the ability to define 2D and 3D structural representations essential for seismic hazard evaluation.

  15. 3D Tomographic Imaging of the Crustal Velocity Structure beneath the Marmara Sea using Air-gun and Earthquake Data

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  16. 3D seismic velocity structure in the rupture area of the 2014 M8.2 Iquique earthquake in Northern Chile

    NASA Astrophysics Data System (ADS)

    Woollam, Jack; Fuenzallida, Amaya; Garth, Tom; Rietbrock, Andreas; Ruiz, Sergio; Tavera, Hernando

    2016-04-01

    Seismic velocity tomography is one of the key tools in Earth sciences to image the physical properties of the subsurface. In recent years significant advances have been made to image the Chilean subductions zone, especially in the area of the 2010 M8.8 Maule earthquake (e.g. Hicks et al., 2014), providing much needed physical constraints for earthquakes source inversions and rupture models. In 2014 the M8.2 Iquique earthquake struck the northern part of the Chilean subduction zone in close proximity to the Peruvian boarder. The pre- and aftershock sequence of this major earthquake was recorded by a densified seismological network in Northern Chile and Southern Peru, which provides an excellent data set to study in depth the 3D velocity structure along the subduction megathrust. Based on an automatic event catalogue of nearly 10,000 events spanning the time period March to May 2014 we selected approximately 450 events for a staggered 3D inversion approach. Events are selected to guarantee an even ray coverage through the inversion volume. We only select events with a minimum GAP of 200 to improve depth estimates and therefore increase resolution in the marine forearc. Additionally, we investigate secondary arrivals between the P- and S-wave arrival to improve depth location. Up to now we have processed about 450 events, from which about 150 with at least 30 P- and S-wave observations have been selected for the subsequent 3D tomography. Overall the data quality is very high, which allows arrival time estimates better than 0.05s on average. We will show results from the 1D, 2D, and preliminary 3D inversions and discuss the results together with the obtained seismicity distribution.

  17. 3D Simultaneous Traveltime Inversion for Velocity Structure, Hypocenter Locations, and Reflector Geometry Using Multiple Classes of Arrivals

    NASA Astrophysics Data System (ADS)

    Bai, Chao-ying; Huang, Guo-jiao; Li, Xing-wang; Greenhalgh, Stewart

    2015-10-01

    Traditionally, traveltime tomography entails inversion of either the velocity field and the reflector geometry sequentially, or the velocity field and the hypocenter locations simultaneously or in a cascaded fashion, but seldom are all three types (velocities, geometry of reflectors, and source locations) updated simultaneously because of the compromise between the different classes of model variable and the lack of different seismic phases to constrain these variables. By using a state-of-the-art ray-tracing algorithm for the first and later arrivals combined with a popular linearized inversion solver, it is possible to simultaneously recover the three classes of model variables. In the work discussed in this paper we combined the multistage irregular shortest-path ray-tracing algorithm with a subspace inversion solver to achieve simultaneous inversion of multi-class variables, using arrival times for different phases to concurrently obtain the velocity field, the reflector shapes, and the hypocenter locations. Simulation and comparison tests for two sets of source-receiver arrangements (one the ideal case and the other an approximated real case) indicate that the combined triple-class inversion algorithm is capable of obtaining nearly the same results as the double-class affect inversion scheme (velocity and reflector geometry, or velocity and source locations) even if a lower ray density and irregular source-receiver geometry are used to simulate the real situation. In addition, the new simultaneous inversion method is not sensitive to a modest amount of picking error in the traveltime data and reasonable uncertainty in earthquake hypocenter locations, which shows it to be a feasible and promising approach in real applications.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  19. 3-D Crustal Velocity Structure of Central Idaho/ Eastern Oregon from Joint Inversion of Rayleigh Wave Group and Phase Velocities Derived from Ambient Seismic Noise: Newest Results from the IDOR Project

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  20. New constraints on the 3D shear wave velocity structure of the upper mantle underneath Southern Scandinavia revealed from non-linear tomography

    NASA Astrophysics Data System (ADS)

    Wawerzinek, B.; Ritter, J. R. R.; Roy, C.

    2013-08-01

    We analyse travel times of shear waves, which were recorded at the MAGNUS network, to determine the 3D shear wave velocity (vS) structure underneath Southern Scandinavia. The travel time residuals are corrected for the known crustal structure of Southern Norway and weighted to account for data quality and pick uncertainties. The resulting residual pattern of subvertically incident waves is very uniform and simple. It shows delayed arrivals underneath Southern Norway compared to fast arrivals underneath the Oslo Graben and the Baltic Shield. The 3D upper mantle vS structure underneath the station network is determined by performing non-linear travel time tomography. As expected from the residual pattern the resulting tomographic model shows a simple and continuous vS perturbation pattern: a negative vS anomaly is visible underneath Southern Norway relative to the Baltic Shield in the east with a contrast of up to 4% vS and a sharp W-E dipping transition zone. Reconstruction tests reveal besides vertical smearing a good lateral reconstruction of the dipping vS transition zone and suggest that a deep-seated anomaly at 330-410 km depth is real and not an inversion artefact. The upper part of the reduced vS anomaly underneath Southern Norway (down to 250 km depth) might be due to an increase in lithospheric thickness from the Caledonian Southern Scandes in the west towards the Proterozoic Baltic Shield in Sweden in the east. The deeper-seated negative vS anomaly (330-410 km depth) could be caused by a temperature anomaly possibly combined with effects due to fluids or hydrous minerals. The determined simple 3D vS structure underneath Southern Scandinavia indicates that mantle processes might influence and contribute to a Neogene uplift of Southern Norway.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  3. A 3-D velocity structure in and around the Miura peninsula, Japan, using a 3-component off-line seismographic array.

    NASA Astrophysics Data System (ADS)

    Kawamura, T.; Hirata, N.; Sato, H.; Onishi, M.; Noda, K.; Saito, H.

    2004-12-01

    A deep seismic profiling around the Metropolitan Tokyo region, the Kanto district, started in 2002 under the project titled as the Regional Characterization of the Crust in Metropolitan Areas for Prediction of Strong Ground Motion. The deep seismic profiling, Tokyo Bay 2003, was performed along the major axis of the Tokyo Bay. Because the seismic line in the Miura peninsula passes through a densely populated area, we have a low signal-to-noise ratio data due to the cultural noise. Thus, in addition to the conventional reflection profiling, we deployed 51 off-line recorders with a 3-compornent geophone of 4.5 Hz at carefully selected, quiet receiver points. During 90 days, we had continuous records including many shot signals produced by vibrators on land and air-guns at the bay area. These data provided far-offset first arrival signals and wide angle reflections. We focus on the common receiver gather records of the Tokyo Bay 2003 off-line stations data to identify first arrival and wide angle phases. We applied the first arrival tomography method using a finite difference travel time solver (Hole, 1992) to those data to obtain a 3-D P-wave velocity structure of the uppermost crust along the profile. We obtained a velocity model in and around the Miura peninsula as follows: Across the Tokyo Bay, near surface is a layer with velocities of 2.0-2.5 km/s. A low velocity area corresponds to the fore-arc basin sediment (post Early Miocene) which extends to a depth of approximately 4 km. High velocity patches are located at a depth of approximately 6 km under the Miura peninsula, which we interpreted as Pre-Neogene basement rocks. Finally, the velocity structure obtained by the tomography analysis is used to improve the processing of the reflection profiling data to clarify the deeper structure in the peninsula, including a good velocity constraint for a pre-stack migration of the reflection profiling data.

  4. 3-D P-wave velocity structure and seismicity in Central Costa Rica from Local Earthquake Tomography using an amphibic network

    NASA Astrophysics Data System (ADS)

    Arroyo, I.; Husen, S.; Flueh, E.; Alvarado, G. E.

    2008-12-01

    The Central Pacific sector of the erosional margin in Costa Rica shows a high seismicity rate, coincident with the subduction of rough-relief ocean floor, and generates earthquakes up to Mw 7. Precise earthquake locations and detailed knowledge of the 3-D velocity structure provide key insights into the dynamics of subduction zones. To this end, we performed a 3-D Local Earthquake Tomography using P-wave traveltimes from 595 selected events recorded by a seismological network of off- and onshore stations, deployed for 6 months in the area. The results reflect the complexity associated to subduction of bathymetric highs and the transition from normal to thickened oceanic crust (Cocos Ridge). The slab is imaged as a high-velocity anomaly with a band of low velocities (LVB) on top enclosing the intraslab events deeper than ~30 km. Below the margin slope, the LVB is locally thickened by at least two seamounts. We observe an abrupt, eastward widening of the LVB, preceded by a low-velocity anomaly under the continental shelf, which we interpret as a big seamount. The thickening coincides with an inverted basin at the inner forearc and a low-velocity anomaly under it. The latter appears in a sector where blocks of inner forearc are uplifted, possibly by underplating of eroded material against the base of the crust. The anomaly promotes seismicity by high-friction with the upper plate, and could be linked to a Mw 6.4 earthquake in 2004. In the west part of the area, the interplate seismicity forms a cluster beneath the continental shelf. Its updip limit coincides with the 150° C isotherm and an increase in Vp along the plate boundary. This further supports a proposed model in which the seismicity onset along the plate interface is mainly due to a decrease in the abundance of the fluids released by subducted sediments. Higher seismicity rates locally concur with seamounts present at the seismogenic zone, while seamounts under the margin slope may shallow the onset of

  5. Multi-scale Finite-Frequency Travel-time Tomography Applied to Imaging 3-D Velocity Structure of the Upper Mantle Beneath the Southwest United States

    NASA Astrophysics Data System (ADS)

    Yin, Y.; Hung, S.

    2007-12-01

    Seismic tomographic imaging has played a key component to unravel the deep processes that caused the surface morphology and rift magmatism in the southwest United States. Several studies used teleseismic body- wave arrivals recorded by the La Ristra experiment, a dense broadband array of 950-km in length deployed during 1999-2001 and run through the Great Plains, the Rio Grande Rift, and the Colorado Plateau, to construct a 2-D tomographic image of the upper mantle structure beneath this linear array (e.g., Gao et al., 2004). However, because of the inevitable smoothing and damping imposed in the tomographic model, the resulting velocity contrast is too weak to explain distinct P and S waveform changes across the array (Song and Helmberger, 2007). In this study, we include all the data from the La Ristra and available nearby arrays and reexamine finite- frequency travel time delays measured by inter-station cross correlation of waveforms at both high- (0.3-2 Hz for P and 0.1-0.5 Hz for S) and low-frequencies (0.03-0.125 Hz for P and 0.03-0.1 Hz for S). Differing from the previous models that rely on classical ray theory and simple grid parameterization, our inversion considers more realistic 3-D sensitivity kernels for relative travel-time delays and a wavelet-based, multi-scale parameterization that enables to yield robust features with spatially-varying resolutions. Our preliminary P-wave model reveals a prominent low-velocity zone extending from near surface to the depth of 300 km beneath the Rio Grande Rift, while the upper mantle which underlies the Great Plains and the Colorado Plateau is seismically fast. We will demonstrate the difference and improvement of 3-D tomographic models through the use of finite-frequency kernels and multi-scale parameterization.

  6. Can we trace the eastern Gondwanan margin in Australia? New perspectives from transdimensional inversion of ambient noise for 3D shear velocity structure

    NASA Astrophysics Data System (ADS)

    Pilia, S.; Rawlinson, N.; Direen, N. G.

    2013-12-01

    Although the notion of Rodinia is quite well accepted in the geoscience community, the location and nature of the eastern continental margin of the Gondwana fragment in Australia is still vague and remains one of the most hotly debated topics in Australian geology. Moreover, most post-Rodinian reconstructions models choose not to tackle the ';Tasmanian challenge', and focus only on the tectonic evolution of mainland southeast Australia, thereby conveniently ignoring the wider tectonic implications of Tasmania's complex geological history. One of the chief limitations of the tectonic reconstructions in this region is a lack of information on Paleozoic (possibly Proterozoic) basement structures. Vast Mesozoic-Cainozoic sedimentary and volcanic cover sequences obscure older outcrops and limit the power of direct observational techniques. In response to these challenges, our effort is focused on ambient seismic noise for imaging 3D crustal shear velocity structure using surface waves, which is capable of illuminating basement structure beneath younger cover. The data used in this study is sourced from the WOMBAT transportable seismic array, which is compounded by around 650 stations spanning the majority of southeastern Australia, including Tasmania and several islands in Bass Strait. To produce the highest quality Green's functions, careful processing of the data has been performed, after which group velocity dispersion measurements have been carried out using a frequency-time analysis method on the symmetric component of the empirical Green's functions (EGFs). Group dispersion measurements from the EGFs have been inverted using a novel hierarchical, transdimensional, Bayesian algorithm to obtain Rayleigh-wave group velocity maps at different periods from 2 to 30 s. The new approach has several advantages in that the number and distribution of model parameters are implicitly controlled by the data, in which the noise is treated as unknown in the inversion. This

  7. 3D velocity structure of the outer forearc of the Colombia-Ecuador subduction zone; implications for the 1958 megathrust earthquake rupture zone

    NASA Astrophysics Data System (ADS)

    Galve, A.; Charvis, P.; Garcia Cano, L.; Marcaillou, B.

    2013-12-01

    In 2005, we conducted an onshore-offshore 3D refraction and wide-angle reflection seismic experiment over the rupture zone of the 1958 subduction earthquake that occurred near the border between Colombia and Ecuador. This earthquake was part of a sequence of 3 large ruptures (1942, Mw=7.8; 1958, Mw=7.7; 1979, Mw=8.2), which successively broke from south to north the segments of the megathrust that had been ruptured in 1906 by a single, very large magnitude (8.8) earthquake. Using first arrival traveltime inversion, we constructed a well-defined Vp velocity model of the plate boundary and of the upper and lower plates, down to 25 km depth. The model reveals a 5-km thick, low velocity zone in the upper plate, located immediately above the interplate contact. Because similar low-velocity zones are commonly observed along margins made of oceanic or island-arc accreted terranes, we suggest that the low-velocity zone might result from the alteration and hydration of mafic and ultramafic rocks in the upper plate basement, rather than from hydrofracturing alone. Sediments underplated beneath the inner wedge might contribute to the low-velocity zone but it is unlikely that they are several kilometers thick. Nevertheless, fluids expelled by the compaction and dehydration of those underplated sediments possibly favor the alteration of the overlying rocks. The low-velocity zone is spatially coincident with the 1958 rupture area. Near the toe of the margin, the model shows a low velocity gradient in the outer wedge that we interpret as a zone of highly faulted and fractured rocks or of poorly consolidated sediments. This low velocity/low gradient region forms the oceanward limit of the rupture zones of both the 1958 and the 1979 earthquakes. We suggest that the two earthquake ruptures were arrested by the low velocity zone because its low rigidity contributed to dissipate most of the seismic energy and of the coseismic strain/stress. This might be the reason why the 1958

  8. A Detailed 3D Seismic Velocity Structure of the Subducting Pacific Slab Beneath Hokkaido, Tohoku and Kanto, Japan, by Double-Difference Tomography

    NASA Astrophysics Data System (ADS)

    Tsuji, Y.; Nakajima, J.; Kita, S.; Okada, T.; Matsuzawa, T.; Hasegawa, A.

    2007-12-01

    Three-dimensional heterogeneous structure beneath northeastern (NE) Japan has been investigated by previous studies and an inclined seismic low-velocity zone is imaged in the mantle wedge sub-parallel to the down-dip direction of the subducting slab (Zhao et al., 1992, Nakajima et al., 2001). However, the heterogeneous structure within the slab has not been well studied even though it is very important to understand the whole process of water transportation from the slab to the surface. Here we show a detailed 3D seismic velocity structure within the subducted Pacific slab around Japan and propose a water-transportation path from the slab to the mantle wedge. In this study, we estimated 3D velocity structure within the Pacific slab by the double-difference tomography (Zhang and Thurber, 2003). We divided the study area, from Hokkaido to Kanto, into 6 areas due to the limitation of memory and computation time. In each area, arrival-time data of 7,500-17,000 events recorded at 70-170 stations were used in the analysis. The total number of absolute travel-time data was about 140,000-312,000 for P wave and 123,000-268,000 for S wave, and differential data were about 736,000-1,920,000 for P wave and 644,000-1,488,000 for S wave. Horizontal and vertical grid separations are 10-25 km and 6.5 km, respectively. RMS residuals of travel times for P wave decreased from 0.23s to 0.09s and for S wave from 0.35s to 0.13s. The obtained results are as follows: (1) a remarkable low-Vs zone exists in the uppermost part of the subducting slab, (2) it extends down to a depth of about 80 km, (3) the termination of this low-Vs zone almost corresponds to the "seismic belt" recently detected in the upper plane of the double seismic zone (Kita et al.,2006; Hasegawa et al., 2007), (4) at depths deeper than 80 km, a low-Vs and high-Vp/Vs zone is apparently distributed in the mantle wedge, immediately above the slab crust. We consider that these features reflect water-transportation processes

  9. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

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

  10. 3D finite element simulations of high velocity projectile impact

    NASA Astrophysics Data System (ADS)

    Ožbolt, Joško; İrhan, Barış; Ruta, Daniela

    2015-09-01

    An explicit three-dimensional (3D) finite element (FE) code is developed for the simulation of high velocity impact and fragmentation events. The rate sensitive microplane material model, which accounts for large deformations and rate effects, is used as a constitutive law. In the code large deformation frictional contact is treated by forward incremental Lagrange multiplier method. To handle highly distorted and damaged elements the approach based on the element deletion is employed. The code is then used in 3D FE simulations of high velocity projectile impact. The results of the numerical simulations are evaluated and compared with experimental results. It is shown that it realistically predicts failure mode and exit velocities for different geometries of plain concrete slab. Moreover, the importance of some relevant parameters, such as contact friction, rate sensitivity, bulk viscosity and deletion criteria are addressed.

  11. Imaging Magma Under St. Helens (iMUSH): Details of passive-source seismic deployment and preliminary 3-D velocity structure

    NASA Astrophysics Data System (ADS)

    Ulberg, C. W.; Creager, K. C.; Moran, S. C.; Abers, G. A.; Denlinger, R. P.; Hotovec-Ellis, A. J.; Vidale, J. E.; Kiser, E.; Levander, A.; Schultz, A.

    2014-12-01

    The imaging Magma Under St. Helens (iMUSH) experiment aims to delineate the extent of the magmatic system beneath Mount St. Helens (MSH) in Washington State. The experiment involves active- and passive-source seismology, magnetotellurics, and geochemistry/petrology. Seventy passive-source broadband seismometers were deployed in a 100-km-diameter array centered on MSH, with an average spacing of 10 km, and a planned duration of two years. The deployment over two weeks in June 2014 involved a group of 18 people split into 6 teams. Approximately half of the seismic stations have aircell batteries and/or pole-mounted solar panels in order to maintain power through deep snow at higher elevations during the winter months. Data will be retrieved 2-4 times a year throughout the duration of the experiment. The first service run performed in mid-July 2014 had a 98.4% data recovery. This is one of the largest wide-aperture two-dimensional arrays covering a volcano anywhere. The active-source portion of the experiment successfully set off 23 shots in late-July 2014. These were recorded clearly at permanent stations run by the Pacific Northwest Seismic Network up to 200 km away, and are expected to be well-recorded on many of the 70 broadband seismometers in addition to the 2500 Reftek "Texans" deployed temporarily for this purpose. For the 2-4 weeks of broadband data collected in July, local earthquakes down to magnitude 0 are recorded across the array, with clear P- and S- arrivals. Earthquakes of this size occur daily within 50 km of MSH. We are keeping a careful catalog of all activity in the region for the duration of the iMUSH experiment. We will pick P- and S-wave travel times at the 70 broadband stations from local earthquakes and active shots, for available data from between June and October 2014. We will also use a tomographic code (Preston et al, 2003, Science) to invert the travel times to obtain preliminary earthquake location and 3-D velocity structure.

  12. Measuring the Stellar Halo Velocity Anisotropy With 3D Kinematics

    NASA Astrophysics Data System (ADS)

    Cunningham, Emily C.; Deason, Alis J.; Guhathakurta, Puragra; Rockosi, Constance M.; van der Marel, Roeland P.; Sohn, S. Tony

    2016-08-01

    We present the first measurement of the anisotropy parameter β using 3D kinematic information outside of the solar neighborhood. Our sample consists of 13 Milky Way halo stars with measured proper motions and radial velocities in the line of sight of M31. Proper motions were measured using deep, multi-epoch HST imaging, and radial velocities were measured from Keck II/DEIMOS spectra. We measure β = -0.3-0.9 +0.4, which is consistent with isotropy, and inconsistent with measurements in the solar neighborhood. We suggest that this may be the kinematic signature of a relatively early, massive accretion event, or perhaps several such events.

  13. Identification of source velocities on 3D structures in non-anechoic environments: Theoretical background and experimental validation of the inverse patch transfer functions method

    NASA Astrophysics Data System (ADS)

    Aucejo, M.; Totaro, N.; Guyader, J.-L.

    2010-08-01

    In noise control, identification of the source velocity field remains a major problem open to investigation. Consequently, methods such as nearfield acoustical holography (NAH), principal source projection, the inverse frequency response function and hybrid NAH have been developed. However, these methods require free field conditions that are often difficult to achieve in practice. This article presents an alternative method known as inverse patch transfer functions, designed to identify source velocities and developed in the framework of the European SILENCE project. This method is based on the definition of a virtual cavity, the double measurement of the pressure and particle velocity fields on the aperture surfaces of this volume, divided into elementary areas called patches and the inversion of impedances matrices, numerically computed from a modal basis obtained by FEM. Theoretically, the method is applicable to sources with complex 3D geometries and measurements can be carried out in a non-anechoic environment even in the presence of other stationary sources outside the virtual cavity. In the present paper, the theoretical background of the iPTF method is described and the results (numerical and experimental) for a source with simple geometry (two baffled pistons driven in antiphase) are presented and discussed.

  14. Volcano-tectonic implications of 3-D velocity structures derived from joint active and passive source tomography of the island of Hawaii

    USGS Publications Warehouse

    Park, J.; Morgan, J.K.; Zelt, C.A.; Okubo, P.G.

    2009-01-01

    We present a velocity model of the onshore and offshore regions around the southern part of the island of Hawaii, including southern Mauna Kea, southeastern Hualalai, and the active volcanoes of Mauna Loa, and Kilauea, and Loihi seamount. The velocity model was inverted from about 200,000 first-arrival traveltime picks of earthquakes and air gun shots recorded at the Hawaiian Volcano Observatory (HVO). Reconstructed volcanic structures of the island provide us with an improved understanding of the volcano-tectonic evolution of Hawaiian volcanoes and their interactions. The summits and upper rift zones of the active volcanoes are characterized by high-velocity materials, correlated with intrusive magma cumulates. These high-velocity materials often do not extend the full lengths of the rift zones, suggesting that rift zone intrusions may be spatially limited. Seismicity tends to be localized seaward of the most active intrusive bodies. Low-velocity materials beneath parts of the active rift zones of Kilauea and Mauna Loa suggest discontinuous rift zone intrusives, possibly due to the presence of a preexisting volcanic edifice, e.g., along Mauna Loa beneath Kilauea's southwest rift zone, or alternatively, removal of high-velocity materials by large-scale landsliding, e.g., along Mauna Loa's western flank. Both locations also show increased seismicity that may result from edifice interactions or reactivation of buried faults. New high-velocity regions are recognized and suggest the presence of buried, and in some cases, previously unknown rift zones, within the northwest flank of Mauna Loa, and the south flanks of Mauna Loa, Hualalai, and Mauna Kea. Copyright 2009 by the American Geophysical Union.

  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. Relocations and 3-D Velocity Structure for Aftershocks of the 2000 W. Tottori (Japan) Earthquake and 2001 Gujarat (India) Earthquake, Using Waveform Cross-correlations

    NASA Astrophysics Data System (ADS)

    Enescu, B.; Mori, J.

    2004-12-01

    The newly developed double-difference tomography method (Zhang and Thurber,2003) makes use of both absolute and relative arrival times to produce an improved velocity model and highly accurate hypocenter locations. By using this technique, we relocate the aftershocks of the 2000 Western Tottori earthquake (Mw 6.7) and 2001 Gujarat (Mw 7.7) earthquake and obtain a 3D-velocity model of the aftershock region. The first data set consists of 1035 aftershocks recorded at 62 stations during a period of about a month following the mainshock (Shibutani et al.,2002). In order to get the best arrival times a cross-correlation analysis was used to align the waveforms. The epicentral distribution of the relocated events reveals clear earthquake lineations, some of them close to the mainshock, and an increased clustering. The aftershocks' depth distribution shows a mean shift of the hypocenters' centroid of about 580m; a clear upper cutoff of the seismic activity and some clustering can be also seen. The final P-wave velocity model shows higher-value anomalies in the vicinity of the mainshock's hypocenter, in good agreement with the results of Shibutani et al.(2004). The second data set consists of about 1300 earthquakes, recorded during one week of observations by a Japanese-Indian research team in the aftershock region of the Gujarat earthquake (Sato et al.,2001). Using the double-difference algorithm and waveform cross-correlations, we were able to identify a more clear alignment of hypocenters that define the mainshock's fault and an area of relatively few aftershocks in the region of the mainshock's hypocenter. Both studies demonstrate that the cross-correlation techniques applied for events with inter-event distances as large as 10km and cross correlation coefficients as low as 50% can produce more accurate locations than those determined from catalog phase data. We are going to discuss briefly the critical role of frequency filtering and of the time window used for cross

  17. Visualizing 3D velocity fields near contour surfaces

    SciTech Connect

    Max, N.; Crawfis, R.; Grant, C.

    1994-03-01

    Vector field rendering is difficult in 3D because the vector icons overlap and hide each other. We propose four different techniques for visualizing vector fields only near surfaces. The first uses motion blurred particles in a thickened region around the surface. The second uses a voxel grid to contain integral curves of the vector field. The third uses many antialiased lines through the surface, and the fourth uses hairs sprouting from the surface and then bending in the direction of the vector field. All the methods use the graphite pipeline, allowing real time rotation and interaction, and the first two methods can animate the texture to move in the flow determined by the velocity field.

  18. The USGS 3D Seismic Velocity Model for Northern California

    NASA Astrophysics Data System (ADS)

    Brocher, T. M.; Aagaard, B.; Simpson, R. W.; Jachens, R. C.

    2006-12-01

    We present a new regional 3D seismic velocity model for Northern California for use in strong motion simulations of the 1906 San Francisco and other earthquakes. The model includes compressional-wave velocity (Vp), shear-wave velocity (Vs), density, and intrinsic attenuation (Qp, Qs). These properties were assigned for each rock type in a 3D geologic model derived from surface outcrops, boreholes, gravity and magnetic data, and seismic reflection, refraction, and tomography studies. A detailed description of the model, USGS Bay Area Velocity Model 05.1.0, is available online [http://www.sf06simulation.org/geology/velocitymodel]. For ground motion simulations Vs and Qs are more important parameters than Vp and Qp because the strongest ground motions are generated chiefly by shear and surface wave arrivals. Because Vp data are more common than Vs data, however, we first developed Vp versus depth relations for each rock type and then converted these to Vs versus depth relations. For the most important rock types in Northern California we compiled measurements of Vp versus depth using borehole logs, laboratory measurements on hand samples, seismic refraction profiles, and tomography models. These rock types include Salinian and Sierran granitic rocks, metagraywackes and greenstones of the Franciscan Complex, Tertiary and Mesozoic sedimentary and volcanic rocks, and Quaternary and Holocene deposits (Brocher, USGS OFR 05-1317, 2005). Vp versus depth curves were converted to Vs versus depth curves using new empirical nonlinear relations between Vs and Vp (Brocher, BSSA, 2005). These relations, showing that Poisson's ratio is a nonlinear function of Vp, were similarly based on compilations of diverse Vs and Vp measurements on a large suite of rock types, mainly from California and the Pacific Northwest. The model is distributed in a discretized form with routines to query the model using C++, C, and Fortran 77 programming languages. The geologic model was discretized at

  19. Structured light field 3D imaging.

    PubMed

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

    2016-09-01

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

  20. 3D high resolution mineral phase distribution and seismic velocity structure of the transition zone: predicted by a full spherical-shell compressible mantle convection model

    NASA Astrophysics Data System (ADS)

    Geenen, T.; Heister, T.; Van Den Berg, A. P.; Jacobs, M.; Bangerth, W.

    2011-12-01

    We present high resolution 3D results of the complex mineral phase distribution in the transition zone obtained by numerical modelling of mantle convection. We extend the work by [Jacobs and van den Berg, 2011] to 3D and illustrate the efficiency of adaptive mesh refinement for capturing the complex spatial distribution and sharp phase transitions as predicted by their model. The underlying thermodynamical model is based on lattice dynamics which allows to predict thermophysical properties and seismic wave speeds for the applied magnesium-endmember olivine-pyroxene mineralogical model. The use of 3D geometry allows more realistic prediction of phase distribution and seismic wave speeds resulting from 3D flow processes involving the Earth's transition zone and more significant comparisons with interpretations from seismic tomography and seismic reflectivity studies aimed at the transition zone. Model results are generated with a recently developed geodynamics modeling application based on dealII (www.dealii.org). We extended this model to incorporate both a general thermodynamic model, represented by P,T space tabulated thermophysical properties, and a solution strategy that allows for compressible flow. When modeling compressible flow in the so called truncated anelastic approximation framework we have to adapt the solver strategy that has been proven by several authors to be highly efficient for incompressible flow to incorporate an extra term in the continuity equation. We present several possible solution strategies and discuss their implication in terms of robustness and computational efficiency.

  1. Uncertainty assessment of 3D instantaneous velocity model from stack velocities

    NASA Astrophysics Data System (ADS)

    Emanuele Maesano, Francesco; D'Ambrogi, Chiara

    2015-04-01

    3D modelling is a powerful tool that is experiencing increasing applications in data analysis and dissemination. At the same time the need of quantitative uncertainty evaluation is strongly requested in many aspects of the geological sciences and by the stakeholders. In many cases the starting point for 3D model building is the interpretation of seismic profiles that provide indirect information about the geology of the subsurface in the domain of time. The most problematic step in the 3D modelling construction is the conversion of the horizons and faults interpreted in time domain to the depth domain. In this step the dominant variable that could lead to significantly different results is the velocity. The knowledge of the subsurface velocities is related mainly to punctual data (sonic logs) that are often sparsely distributed in the areas covered by the seismic interpretation. The extrapolation of velocity information to wide extended horizons is thus a critical step to obtain a 3D model in depth that can be used for predictive purpose. In the EU-funded GeoMol Project, the availability of a dense network of seismic lines (confidentially provided by ENI S.p.A.) in the Central Po Plain, is paired with the presence of 136 well logs, but few of them have sonic logs and in some portion of the area the wells are very widely spaced. The depth conversion of the 3D model in time domain has been performed testing different strategies for the use and the interpolation of velocity data. The final model has been obtained using a 4 layer cake 3D instantaneous velocity model that considers both the initial velocity (v0) in every reference horizon and the gradient of velocity variation with depth (k). Using this method it is possible to consider the geological constraint given by the geometries of the horizons and the geo-statistical approach to the interpolation of velocities and gradient. Here we present an experiment based on the use of set of pseudo-wells obtained from the

  2. Towards an Anisotropic Whole Mantle 3D Elastic Velocity Model

    NASA Astrophysics Data System (ADS)

    Panning, M. P.; Romanowicz, B.; Gung, Y.

    2001-12-01

    Many studies have documented the existence of anisotropy in the earth's upper mantle, concentrated in the top 200 km. This evidence comes from the study of surface waves as well as shear wave splitting. There is also evidence for shear wave splitting in D", at least in well sampled regions. There are some hints of anisotropy at the base of the transition zone. Tomographic models of the upper mantle have been developed with simplifying assumptions about the nature of the anisotropy, in order to minimize the number of free parameters in the inversions. Some assume transverse isotropy (e.g Ekström and Dziewonski, 1997), others include additional degrees of freedom with some realistic constraints on mineralogy (e.g. Montagner and Tanimoto, 1991). Our goal is to investigate anisotropy in the whole mantle, using the framework of waveform inversion, and the nonlinear asymptotic mode coupling theory (NACT), previously developed and applied to the construction of whole-mantle SH velocity models (Li and Romanowicz, 1996; Mégnin and Romanowicz, 2000). For this we require a 3 component dataset, and we have extended our automatic transverse (T) component wavepicking procedures to the vertical (Z) and longitudinal (L) component - a non-trivial task given the large number of phases present in the coupled P-SV system. A useful initial assumption, for which the theory has been readily adapted, is that of transverse isotropy. As a first step towards this, we have been investigating inversions using T component and Z,L component data separately. In particular, this allows us to explore the sampling that can be achieved with Z,L component data alone in the deepest part of the mantle. Indeed, D" is in general much better sampled in SH than in SV, owing to the availability of SHdiff at large distances, while SVdiff decays more rapidly due to mantle-core coupling. We present the results of our resolution experiments and discuss the differences between the 3D SV model obtained in well

  3. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

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

  4. Effects of 3D Velocity and Attenuation in the Tonga-Fiji Subduction Zone

    NASA Astrophysics Data System (ADS)

    Savage, B.; Wiens, D. A.; Tromp, J.

    2005-12-01

    The current understanding of a subduction zone's temperature and composition is limited. Much of our recent knowledge of subduction zones comes from earthquake locations, geochemical measurements, and lab based experiments. Recently, two studies of the Tonga-Fiji subduction zone have presented tomographic images of velocity and attenuation (Roth et al., 1999; Zhao et al., 1997). Roth et al. (2000) then combined these two tomographic models of the Tonga-Fiji subduction zone to derive an empirical relationship between changes in velocity and attenuation. This relationship agrees well with two independent, experimental data sets (Jackson et al., 1992; Sato et al., 1989). Using the tomographic velocity model and the empirical relationship between velocity and attenuation we create synthetic seismograms for the Tonga-Fiji subduction zone to test whether a simple increase in velocity accurately depicts this subduction zone. To construct the model we use the tomographic model of Zhao et al. (1997) to create a shear velocity model using a simple Vs/Vp ratio. Following Roth et al. (2000) these tomographic models are combined with the empirical relation between velocity and attenuation to create an attenuation model. The resulting synthetics are compared to recorded data to validate the tomographic velocity model and the empirical relation between velocity and attenuation. Any mismatch in this comparison will provide a basis for further refinement of the tomographic models and the velocity-attenuation relation. The synthetics are created using the SPECFEM3D global code (Komatitsch et al., 2002) with the new addition of a three-dimensional attenuation operator. Attenuation is simulated by a set of standard linear solids over the desired frequency range as described in Liu et al. (1976). Our initial results at a minimum period of 3.3 seconds suggest that the attenuation structure plays a minor role for the present source-receiver geometry. The addition of the 3D attenuation

  5. Congruence of 3-D Whole Mantle Models of Shear Velocity

    NASA Astrophysics Data System (ADS)

    Dziewonski, A. M.; Lekic, V.; Romanowicz, B. A.

    2012-12-01

    The range of shear velocity anomalies in published whole mantle models is considerable. This impedes drawing conclusions of importance for geodynamic modeling and for interpretation of mineral physics results. However, if one considers only the models that were built using data that are sensitive to mantle structure at all depths, these models show robust features in their power spectra as a function of depth. On this basis we propose that there are five depth intervals with distinct spectral characteristics. 1. Heterosphere (Moho - 300 km) is characterized by strong power spectrum relatively flat up to degree 6. With lateral shear wavespeed variations as large as 15%, this zone accounts for more than 50% of the entire heterogeneity in the mantle. Differences among models for different tectonic regions decrease rapidly below 300 km depth. 2. Upper mantle buffer zone (300- 500 km) has a flat spectrum and the overall power of heterogeneity drops by an order of magnitude compared to the region above. There may be still weak difference between continents and oceans, but the oceanic regions lose their age dependence. The spectral characteristics do not change across the 410 km discontinuity. 3. Transition zone (500 - 650 km) The degree 2 anomaly becomes dominant. There are long wavelength anomalies in regions of the fastest plate subduction during the last 15-20 Ma, suggesting slab ponding above the 650 km discontinuity. Several slower-than-average anomalies of unknown origin are present in this depth range. 4. Lower mantle buffer zone (650 - 2300 km) has a weak, flat spectrum without long wavelength velocity anomalies that could be interpreted as unfragmented subducted slabs. However, there are three relatively narrow and short high velocity anomalies under Peru, Tonga and Indonesia that may indicate limited slab penetration. 5 Abyssal layer (2300 - CMB) Strong spectrum dominated by degrees 2 and 3. The amplitude is the largest at the CMB and decreases rapidly up to

  6. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

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

  7. UCVM: Open Source Software for Understanding and Delivering 3D Velocity Models

    NASA Astrophysics Data System (ADS)

    Gill, D.; Small, P.; Maechling, P. J.; Jordan, T. H.; Shaw, J. H.; Plesch, A.; Chen, P.; Lee, E. J.; Taborda, R.; Olsen, K. B.; Callaghan, S.

    2014-12-01

    Physics-based ground motion simulations can calculate the propagation of earthquake waves through 3D velocity models of the Earth. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) framework to help researchers build structured or unstructured velocity meshes from 3D velocity models for use in wave propagation simulations. The UCVM software framework makes it easy to extract P and S wave propagation speeds and other material properties from 3D velocity models by providing a common interface through which researchers can query earth models for a given location and depth. Currently, the platform supports multiple California models, including SCEC CVM-S4 and CVM-H 11.9.1, and has been designed to support models from any region on earth. UCVM is currently being use to generate velocity meshes for many SCEC wave propagation codes, including AWP-ODC-SGT and Hercules. In this presentation, we describe improvements to the UCVM software. The current version, UCVM 14.3.0, released in March of 2014, supports the newest Southern California velocity model, CVM-S4.26, which was derived from 26 full-3D tomographic iterations using CVM-S4 as the starting model (Lee et al., this meeting), and the Broadband 1D velocity model used in the CyberShake 14.2 study. We have ported UCVM to multiple Linux distributions and OS X. Also included in this release is the ability to add small-scale stochastic heterogeneities to extract Cartesian meshes for use in high-frequency ground motion simulations. This tool was built using the C language open-source FFT library, FFTW. The stochastic parameters (Hurst exponent, correlation length, and the horizontal/vertical aspect ratio) can be customized by the user. UCVM v14.3.0 also provides visualization scripts for constructing cross-sections, horizontal slices, basin depths, and Vs30 maps. The interface allows researchers to visually review velocity models . Also, UCVM v14.3.0 can extract

  8. Bayesian 3D velocity field reconstruction with VIRBIUS

    NASA Astrophysics Data System (ADS)

    Lavaux, Guilhem

    2016-03-01

    I describe a new Bayesian-based algorithm to infer the full three dimensional velocity field from observed distances and spectroscopic galaxy catalogues. In addition to the velocity field itself, the algorithm reconstructs true distances, some cosmological parameters and specific non-linearities in the velocity field. The algorithm takes care of selection effects, miscalibration issues and can be easily extended to handle direct fitting of e.g. the inverse Tully-Fisher relation. I first describe the algorithm in details alongside its performances. This algorithm is implemented in the VIRBIUS (VelocIty Reconstruction using Bayesian Inference Software) software package. I then test it on different mock distance catalogues with a varying complexity of observational issues. The model proved to give robust measurement of velocities for mock catalogues of 3000 galaxies. I expect the core of the algorithm to scale to tens of thousands galaxies. It holds the promises of giving a better handle on future large and deep distance surveys for which individual errors on distance would impede velocity field inference.

  9. 3D Simulation of Velocity Profile of Turbulent Flow in Open Channel with Complex Geometry

    NASA Astrophysics Data System (ADS)

    Kamel, Benoumessad; Ilhem, Kriba; Ali, Fourar; Abdelbaki, Djebaili

    Simulation of open channel flow or river flow presents unique challenge to numerical simulators, which is widely used in the applications of computational fluid dynamics. The prediction is extremely difficult because the flow in open channel is usually transient and turbulent, the geometry is irregular and curved, and the free-surface elevation is varying with time. The results from a 3D non-linear k- ɛ turbulence model are presented to investigate the flow structure, the velocity distribution and mass transport process in a meandering compound open channel and a straight open channel. The 3D numerical model for calculating flow is set up in cylinder coordinates in order to calculate the complex boundary channel. The finite volume method is used to disperse the governing equations and the SIMPLE algorithm is applied to acquire the coupling of velocity and pressure. The non-linear k- ɛ turbulent model has good useful value because of taking into account the anisotropy and not increasing the computational time. The main contributions of this study are developing a numerical method that can be applied to predict the flow in river bends with various bend curvatures and different width-depth ratios. This study demonstrates that the 3D non-linear k- ɛ turbulence model can be used for analyzing flow structures, the velocity distribution and pollutant transport in the complex boundary open channel, this model is applicable for real river and wetland problem.

  10. 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

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

    PubMed

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

    2008-01-01

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

  12. 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

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

    PubMed Central

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

    2010-01-01

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

  14. Measurements of 3D slip velocities and plasma column lengths of a gliding arc discharge

    SciTech Connect

    Zhu, Jiajian; Gao, Jinlong; Ehn, Andreas; Aldén, Marcus; Li, Zhongshan E-mail: alpers@ma.tum.de; Moseev, Dmitry; Kusano, Yukihiro; Salewski, Mirko; Alpers, Andreas E-mail: alpers@ma.tum.de; Gritzmann, Peter; Schwenk, Martin

    2015-01-26

    A non-thermal gliding arc discharge was generated at atmospheric pressure in an air flow. The dynamics of the plasma column and tracer particles were recorded using two synchronized high-speed cameras. Whereas the data analysis for such systems has previously been performed in 2D (analyzing the single camera image), we provide here a 3D data analysis that includes 3D reconstructions of the plasma column and 3D particle tracking velocimetry based on discrete tomography methods. The 3D analysis, in particular, the determination of the 3D slip velocity between the plasma column and the gas flow, gives more realistic insight into the convection cooling process. Additionally, with the determination of the 3D slip velocity and the 3D length of the plasma column, we give more accurate estimates for the drag force, the electric field strength, the power per unit length, and the radius of the conducting zone of the plasma column.

  15. 3d Velocity Tomography of The Kos - Nisyros Volcanic Area - East Aegean Sea

    NASA Astrophysics Data System (ADS)

    Nikolova, S.; Ilinski, D.; Makris, J.; Chonia, T.; Stavrakakis, J.

    Since June 2000, active and passive seismic observations have been carried out by IfG, GeoPro GmbH, Hamburg and Institute of Geodynamics, Athens within the frame of the project GEOWARN (Geo-Spacial Warning Systems Nisyros Volcano, Greece: An Emergency Case Study of the Volcanic Area of Nisyros) supported by the European Community. In the active experiment 48 recording seismic units were deployed and recorded more than 7000 shots in 3D array. The Nisyros volcano has been identified as an apophytic intrusion of much larger volcanic structure with a caldera of 35 km diameter, extending between the southern coasts of the islands of Kos and Nisyros. To obtain 3-D velocity structure of the area a tomographic inversion was made using 6800 rays which probed the area with a very high ray density. The method applied and the high accuracy of active tomographic data allowed to resolve the high velocity bodies in the caldera. The complex volcanic structure is identified by high velocity rocks in- truding through the upper crust and penetrating the volcanic cone to depth of approx. 1.0 km to 1.8 km below the surface. Particularly high velocity bodies were identified below the islands of Yali and the central caldera of Nisyros. The high velocity bodies at shallow depth were interpreted as high-density cumulates of solidified magma intru- sion in the caldera. These intrusions explain very high temperature of 300C observed in the lower aquifer in the caldera at 1.5 km depth as confirmed by drilling. The vol- canic edifices of Kos, Yali, Nisyros and Strongily are part of a major volcanic caldera nearly 35 km in diameter. This size of the volcanic caldera explains the large volume of ignimbrites erupted 160 000 years ago. By combining geodetic, geophysical, geo- chemical and geological observations it is intended to correlate magma movements and associated changes of physical and chemical parameters of the recent volcanism.

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

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

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

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

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

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

  18. Probabilistic earthquake location and 3-D velocity models in routine earthquake location

    NASA Astrophysics Data System (ADS)

    Lomax, A.; Husen, S.

    2003-12-01

    Earthquake monitoring agencies, such as local networks or CTBTO, are faced with the dilemma of providing routine earthquake locations in near real-time with high precision and meaningful uncertainty information. Traditionally, routine earthquake locations are obtained from linearized inversion using layered seismic velocity models. This approach is fast and simple. However, uncertainties derived from a linear approximation to a set of non-linear equations can be imprecise, unreliable, or even misleading. In addition, 1-D velocity models are a poor approximation to real Earth structure in tectonically complex regions. In this paper, we discuss the routine location of earthquakes in near real-time with high precision using non-linear, probabilistic location methods and 3-D velocity models. The combination of non-linear, global search algorithms with probabilistic earthquake location provides a fast and reliable tool for earthquake location that can be used with any kind of velocity model. The probabilistic solution to the earthquake location includes a complete description of location uncertainties, which may be irregular and multimodal. We present applications of this approach to determine seismicity in Switzerland and in Yellowstone National Park, WY. Comparing our earthquake locations to earthquake locations obtained using linearized inversion and 1-D velocity models clearly demonstrates the advantages of probabilistic earthquake location and 3-D velocity models. For example, the more complete and reliable uncertainty information of non-linear, probabilistic earthquake location greatly facilitates the identification of poorly constrained hypocenters. Such events are often not identified in linearized earthquake location, since the location uncertainties are determined with a simplified, localized and approximate Gaussian statistic.

  19. Imaging 3D seismic velocity along the seismogenic zone of Algarve region (southern Portugal)

    NASA Astrophysics Data System (ADS)

    Rocha, João.; Bezzeghoud, Mourad; Caldeira, Bento; Dias, Nuno; Borges, José; Matias, Luís.; Dorbath, Catherine; Carrilho, Fernando

    2010-05-01

    The present seismic tomographic study is focused around Algarve region, in South of Portugal. To locate the seismic events and find the local velocity structure of epicentral area, the P and S arrival times at 38 stations are used. The data used in this study were obtained during the Algarve campaign which worked from January/2006 to July/2007. The preliminary estimate of origin times and hypocentral coordinates are determined by the Hypoinverse program. Linearized inversion procedure was applied to comprise the following two steps: 1) finding the minimum 1D velocity model using Velest and 2) simultaneous relocation of hypocenters and determination of local velocity structure. The velocity model we have reached is a 10 layer model which gave the lowest RMS, after several runnings of eight different velocity models that we used "a priori". The model parameterization assumes a continuous velocity field between 4.5 km/s and 7.0 km/s until 30 km depth. The earth structure is represented in 3D by velocity at discrete points, and velocity at any intervening point is determined by linear interpolation among the surrounding eight grid points. A preliminary analysis of the resolution capabilities of the dataset, based on the Derivative Weight Sum (DWS) distribution, shows that the velocity structure is better resolved in the West part of the region between the surface to15 km. The resulting tomographic image has a prominent low-velocity anomaly that shows a maximum decrease in P-wave velocity in the first 12 kms in the studied region. We also identified the occurrence of local seismic events of reduced magnitude not catalogued, in the neighbourhood of Almodôvar (low Alentejo). The spatial distribution of epicentres defines a NE-SW direction that coincides with the strike of the mapped geological faults of the region and issued from photo-interpretation. Is still expectable to refine the seismicity of the region of Almodôvar and establish more rigorously its role in the

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

    PubMed

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

    2015-07-01

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

  1. 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

  2. 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

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

    PubMed

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

    2016-07-01

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

  4. 3-D crustal velocity model for Lithuania and its application to local event studies

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  5. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

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

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

    PubMed Central

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

    2015-01-01

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

  7. Development of a Regional Velocity Model Using 3D Broadband Waveform Sensitivity

    NASA Astrophysics Data System (ADS)

    Panning, M. P.; Romanowicz, B. A.; Kim, A.

    2005-12-01

    We are developing a new approach which relies on a cascade of increasingly accurate theoretical approximations for computation of the seismic wavefield to develop a model of regional seismic velocity structure for eastern Eurasia using full seismic waveforms. The selected area is particularly suitable for the purpose of this experiment, as it is highly heterogeneous, presenting a challenge for standard modeling techniques, but it is well surrounded by earthquake sources and a significant number of high quality broadband digital stations exist, for which data are readily accessible through IRIS (Incorporated Research Institutions for Seismology) and the FDSN (Federation of Digital Seismic Networks). The initial model is derived from a large database of teleseismic long period waveforms (surface waves and overtone wavepackets) using well-developed theoretical approximations, the Path Average Approximation (PAVA) and Nonlinear Asymptotic Coupling Theory (NACT). These approaches assume waveforms are only sensitive to the 1D (PAVA) and 2D (NACT) structure in the vertical plane between source and receiver, which is adequate for the development of a smooth initial 3D velocity model. We refine this model using a more accurate theoretical approach. We utilize an implementation of a 3D Born approximation, which takes into account the contribution to the waveform from single scattering throughout the model, giving full 3D waveform sensitivity kernels. We perform verification tests of this approach for synthetic models, and show that it can accurately represent the wavefield as predicted by numerical approaches in several situations where approximations such as PAVA and NACT are insufficient. The Born 3D waveform sensitivity kernels are used to perform a higher resolution inversion of regional waveforms for a smaller subregion between longitudes 90 and 150 degrees E, and latitudes 15 and 40 degrees N. To further increase the accuracy of this model, we intend to utilize a very

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

    PubMed Central

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

    2010-01-01

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

  9. Effects of 3D random correlated velocity perturbations on predicted ground motions

    USGS Publications Warehouse

    Hartzell, S.; Harmsen, S.; Frankel, A.

    2010-01-01

    Three-dimensional, finite-difference simulations of a realistic finite-fault rupture on the southern Hayward fault are used to evaluate the effects of random, correlated velocity perturbations on predicted ground motions. Velocity perturbations are added to a three-dimensional (3D) regional seismic velocity model of the San Francisco Bay Area using a 3D von Karman random medium. Velocity correlation lengths of 5 and 10 km and standard deviations in the velocity of 5% and 10% are considered. The results show that significant deviations in predicted ground velocities are seen in the calculated frequency range (≤1 Hz) for standard deviations in velocity of 5% to 10%. These results have implications for the practical limits on the accuracy of scenario ground-motion calculations and on retrieval of source parameters using higher-frequency, strong-motion data.

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

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  12. 3-D crustal velocity model for Lithuania and its application to local event studies

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  13. The 3D Space and Spin Velocities of a Gamma-ray Pulsar

    NASA Astrophysics Data System (ADS)

    Romani, Roger W.

    2016-04-01

    PSR J2030+4415 is a LAT-discovered 0.5My-old gamma-ray pulsar with an X-ray synchrotron trail and a rare Halpha bowshock. We have obtained GMOS IFU spectroscopic imaging of this shell, and show a sweep through the remarkable Halpha structure, comparing with the high energy emission. These data provide a unique 3D map of the momentum distribution of the relativistic pulsar wind. This shows that the pulsar is moving nearly in the plane of the sky and that the pulsar wind has a polar component misaligned with the space velocity. The spin axis is shown to be inclined some 95degrees to the Earth line of sight, explaining why this is a radio-quiet, gamma-only pulsar. Intriguingly, the shell also shows multiple bubbles that suggest that the pulsar wind power has varied substantially over the past 500 years.

  14. A New Regional 3-D Velocity Model of the India-Pakistan Region for Improved Event Location Accuracy

    NASA Astrophysics Data System (ADS)

    Reiter, D.; Vincent, C.; Johnson, M.

    2001-05-01

    A 3-D velocity model for the crust and upper mantle (WINPAK3D) has been developed to improve regional event location in the India-Pakistan region. Results of extensive testing demonstrate that the model improves location accuracy for this region, specifically for the case of small regionally recorded events, for which teleseismic data may not be available. The model was developed by integrating the results of more than sixty previous studies related to crustal velocity structure in the region. We evaluated the validity of the 3-D model using the following methods: (1) cross validation analysis for a variety of events, (2) comparison of model determined hypocenters with known event location, and (3) comparison of model-derived and empirically-derived source-specific station corrections (SSSC) generated for the International Monitoring System (IMS) auxiliary seismic station located at Nilore. The 3-D model provides significant improvement in regional location compared to both global and regional 1-D models in this area of complex structural variability. For example, the epicenter mislocation for an event with a well known location was only 6.4 km using the 3-D model, compared with a mislocation of 13.0 km using an average regional 1-D model and 15.1 km for the IASPEI91 model. We will present these and other results to demonstrate that 3-D velocity models are essential to improving event location accuracy in regions with complicated crustal geology and structures. Such 3-D models will be a prerequisite for achieving improved location accuracies for regions of high monitoring interest.

  15. 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.

  16. Velocity and Density Models Incorporating the Cascadia Subduction Zone for 3D Earthquake Ground Motion Simulations

    USGS Publications Warehouse

    Stephenson, William J.

    2007-01-01

    INTRODUCTION In support of earthquake hazards and ground motion studies in the Pacific Northwest, three-dimensional P- and S-wave velocity (3D Vp and Vs) and density (3D rho) models incorporating the Cascadia subduction zone have been developed for the region encompassed from about 40.2?N to 50?N latitude, and from about -122?W to -129?W longitude. The model volume includes elevations from 0 km to 60 km (elevation is opposite of depth in model coordinates). Stephenson and Frankel (2003) presented preliminary ground motion simulations valid up to 0.1 Hz using an earlier version of these models. The version of the model volume described here includes more structural and geophysical detail, particularly in the Puget Lowland as required for scenario earthquake simulations in the development of the Seattle Urban Hazards Maps (Frankel and others, 2007). Olsen and others (in press) used the model volume discussed here to perform a Cascadia simulation up to 0.5 Hz using a Sumatra-Andaman Islands rupture history. As research from the EarthScope Program (http://www.earthscope.org) is published, a wealth of important detail can be added to these model volumes, particularly to depths of the upper-mantle. However, at the time of development for this model version, no EarthScope-specific results were incorporated. This report is intended to be a reference for colleagues and associates who have used or are planning to use this preliminary model in their research. To this end, it is intended that these models will be considered a beginning template for a community velocity model of the Cascadia region as more data and results become available.

  17. 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.

  18. Validating 3D Seismic Velocity Models Using the Spectral Element Method

    NASA Astrophysics Data System (ADS)

    Maceira, M.; Rowe, C. A.; Allen, R. M.; Obrebski, M. J.

    2010-12-01

    As seismic instrumentation, data storage and dissemination and computational power improve, seismic velocity models attempt to resolve smaller structures and cover larger areas. However, it is unclear how accurate these velocity models are and, while the best models available are used for event determination, it is difficult to put uncertainties on seismic event parameters. Model validation is typically done using resolution tests that assume the imaging theory used is accurate and thus only considers the impact of the data coverage on resolution. We present the results of a more rigorous approach to model validation via full three-dimensional waveform propagation using Spectral Element Methods (SEM). This approach makes no assumptions about the theory used to generate the models but require substantial computational resources. We first validate 3D tomographic models for the Western USA generated using both ray-theoretical and finite-frequency methods. The Dynamic North America (DNA) Models of P- and S- velocity structure (DNA09-P and DNA09-S) use teleseismic body-wave traveltime residuals recorded at over 800 seismic stations provided by the Earthscope USArray and regional seismic networks. We performed systematic computations of synthetics for the dataset used to generate the DNA models. Direct comparison of these synthetic seismograms to the actual observations allows us to accurately assess and validate the models. Implementation of the method for a densely instrumented region such as that covered by the DNA model provides a useful testbed for the validation methods that we will subsequently apply to other, more challenging study areas.

  19. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

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

  20. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

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

    2010-01-01

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

  1. Effect of postural changes on 3D joint angular velocity during starting block phase.

    PubMed

    Slawinski, Jean; Dumas, Raphaël; Cheze, Laurence; Ontanon, Guy; Miller, Christian; Mazure-Bonnefoy, Alice

    2013-01-01

    Few studies have focused on the effect of posture during sprint start. The aim of this study was to measure the effect of the modification of horizontal distance between the blocks during sprint start on three dimensional (3D) joint angular velocity. Nine trained sprinters started using three different starting positions (bunched, medium and elongated). They were equipped with 63 passive reflective markers, and an opto-electronic Motion Analysis system was used to collect the 3D marker trajectories. During the pushing phase on the blocks, norm of the joint angular velocity (NJAV), 3D Euler angular velocity (EAV) and pushing time on the blocks were calculated. The results demonstrated that the decrease of the block spacing induces an opposite effect on the angular velocity of joints of the lower and the upper limbs. The NJAV of the upper limbs is greater in the bunched start, whereas the NJAV of the lower limbs is smaller. The modifications of NJAV were due to a combination of the movement of the joints in the different degrees of freedom. The medium start seems to be the best compromise because it leads, in a short pushing time, to a combination of optimal joint velocities for upper and lower segments. PMID:23062070

  2. 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).

  3. UCVM: An Open Source Software Package for Querying and Visualizing 3D Velocity Models

    NASA Astrophysics Data System (ADS)

    Gill, D.; Small, P.; Maechling, P. J.; Jordan, T. H.; Shaw, J. H.; Plesch, A.; Chen, P.; Lee, E. J.; Taborda, R.; Olsen, K. B.; Callaghan, S.

    2015-12-01

    Three-dimensional (3D) seismic velocity models provide foundational data for ground motion simulations that calculate the propagation of earthquake waves through the Earth. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) package for both Linux and OS X. This unique framework provides a cohesive way for querying and visualizing 3D models. UCVM v14.3.0, supports many Southern California velocity models including CVM-S4, CVM-H 11.9.1, and CVM-S4.26. The last model was derived from 26 full-3D tomographic iterations on CVM-S4. Recently, UCVM has been used to deliver a prototype of a new 3D model of central California (CCA) also based on full-3D tomographic inversions. UCVM was used to provide initial plots of this model and will be used to deliver CCA to users when the model is publicly released. Visualizing models is also possible with UCVM. Integrated within the platform are plotting utilities that can generate 2D cross-sections, horizontal slices, and basin depth maps. UCVM can also export models in NetCDF format for easy import into IDV and ParaView. UCVM has also been prototyped to export models that are compatible with IRIS' new Earth Model Collaboration (EMC) visualization utility. This capability allows for user-specified horizontal slices and cross-sections to be plotted in the same 3D Earth space. UCVM was designed to help a wide variety of researchers. It is currently being use to generate velocity meshes for many SCEC wave propagation codes, including AWP-ODC-SGT and Hercules. It is also used to provide the initial input to SCEC's CyberShake platform. For those interested in specific data points, the software framework makes it easy to extract P and S wave propagation speeds and other material properties from 3D velocity models by providing a common interface through which researchers can query earth models for a given location and depth. Also included in the last release was the ability to add small

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

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

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

  5. Mapping Faults from 3-D Tomographic Velocity Model using Image Processing / Computer Vision Algorithms: Application to Northern Cascadia

    NASA Astrophysics Data System (ADS)

    Ramachandran, K.

    2011-12-01

    Three dimensional velocity models constructed through seismic tomography are seldom digitally processed further for imaging structural features. A study conducted to evaluate the potential for imaging subsurface discontinuities in horizontal and vertical direction from three dimensional velocity models using image processing/computer vision techniques has provided significant results. Three-dimensional velocity models constructed through tomographic inversion of active source and/or earthquake traveltime data are generally built from an initial 1-D velocity model that varies only with depth. Regularized tomographic inversion algorithms impose constraints on the roughness of the model that help to stabilize the inversion process. Final velocity models obtained from regularized tomographic inversions have smooth three-dimensional structures that are required by the data. Final velocity models are usually analyzed and interpreted either as a perturbation velocity model or as an absolute velocity model. Compared to perturbation velocity model, absolute velocity model has an advantage of providing constraints on lithology. Both velocity models lack the ability to provide sharp constraints on subsurface faults. However, results from the analysis of the 3-D velocity model from northern Cascadia using Roberts, Prewitt, Sobel, and Canny operators show that subsurface faults that are not clearly interpretable from velocity model plots can be identified through this approach. This analysis resulted in inferring the locations of Tacoma Fault, Seattle Fault, Southern Whidbey Island Fault, and Darrington Devils Mountain fault much clearly. The Coast Range Boundary Fault, previously hypothesized on the basis of sedimentological and tectonic observations is inferred clearly from processed images. Many of the fault locations so imaged correlate with earthquake hypocenters indicating their seismogenic nature.

  6. 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.

  7. 3D visualization of endocardial peak velocities during systole and diastole

    NASA Astrophysics Data System (ADS)

    Eusemann, Christian D.; Ritman, Erik L.; Robb, Richard A.

    2002-04-01

    Quantitative assessment of regional heart motion has the potential to provide diagnostic data for assessment of cardiac malfunction. Local heart motion may be obtained with various medical imaging scanners, so the goal is to provide an imaging modality-independent display/analysis technique. In this study, 3D reconstructions of a canine heart before and after infarction were obtained from the Dynamic Spatial Reconstructor (DSR) at 15 time points throughout one cardiac cycle. Deformable models of each time point were created. Through this process regional excursions and velocities in the mesh can be assigned to represent a piece of endocardium, which can be calculated for each time-point interval. These calculations are based on the distance change between a single vertex of the mesh and the model centerline from LV apex to aortic/mitral valve separation. This allows computation of color maps corresponding to regional values of contraction or dilation motion of the endocardium relative to the LV long axis (centerline) during systole and/or diastole. These color maps can be illustrated through model animations and multi view static images. Using functional parametric mappings of disturbances in regional contractility and relaxation facilitates appreciation of the effect of altered structure-to-function relationships in the myocardium.

  8. Capacitance extraction from complex 3D interconnect structures

    SciTech Connect

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

    1999-06-01

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

  9. 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.

  10. 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.

  11. A 3-D shear velocity model of the southern North American and Caribbean plates from ambient noise and earthquake tomography

    NASA Astrophysics Data System (ADS)

    Gaite, B.; Villaseñor, A.; Iglesias, A.; Herraiz, M.; Jiménez-Munt, I.

    2015-02-01

    We use group velocities from earthquake tomography together with group and phase velocities from ambient noise tomography (ANT) of Rayleigh waves to invert for the 3-D shear-wave velocity structure (5-70 km) of the Caribbean (CAR) and southern North American (NAM) plates. The lithospheric model proposed offers a complete image of the crust and uppermost-mantle with imprints of the tectonic evolution. One of the most striking features inferred is the main role of the Ouachita-Marathon-Sonora orogeny front on the crustal seismic structure of the NAM plate. A new imaged feature is the low crustal velocities along the USA-Mexico border. The model also shows a break of the east-west mantle velocity dichotomy of the NAM and CAR plates beneath the Isthmus of the Tehuantepec and the Yucatan Block. High upper-mantle velocities along the Mesoamerican Subduction Zone coincide with inactive volcanic areas while the lowest velocities correspond to active volcanic arcs and thin lithospheric mantle regions.

  12. Probabilistic Seismic Hazard Maps of Seattle, Washington, Including 3D Sedimentary Basin Effects and Rupture Directivity: Implications of 3D Random Velocity Variations (Invited)

    NASA Astrophysics Data System (ADS)

    Frankel, A. D.; Stephenson, W. J.; Carver, D.; Odum, J.; Williams, R. A.; Rhea, S.

    2010-12-01

    We have produced probabilistic seismic hazard maps of Seattle for 1 Hz spectral acceleration, using over five hundred 3D finite-difference simulations of earthquakes on the Seattle fault, Southern Whidbey Island fault, and Cascadia subduction zone, as well as for random deep and shallow earthquakes at various locations. The 3D velocity model was validated by modeling the observed waveforms for the 2001 M6.8 Nisqually earthquake and several smaller events in the region. At these longer periods (≥ 1 sec) that are especially important to the response of buildings of ten stories or higher, seismic waves are strongly influenced by sedimentary basins and rupture directivity. We are investigating how random spatial variations in the 3D velocity model affect the simulated ground motions for M6.7 earthquakes on the Seattle fault. A fractal random variation of shear-wave velocity with a Von Karman correlation function produces spatial variations of peak ground velocity with multiple scale lengths. We find that a 3D velocity model with a 10% standard deviation in shear-wave velocity in the top 1.5 km and 5% standard deviation from 1.5-10 km depth produces variations in peak ground velocities of as much as a factor of two, relative to the case with no random variations. The model with random variations generally reduces the peak ground velocity of the forward rupture directivity pulse for sites near the fault where basin-edge focusing of S-waves occurs. It also tends to reduce the peak velocity of localized areas where basin surface waves are focused. However, the medium with random variations also causes small-scale amplification of ground motions over distances of a few kilometers. We are also evaluating alternative methods of characterizing the aleatory uncertainty in the probabilistic hazard calculations.

  13. 3D velocity measurements in a premixed flame by tomographic PIV

    NASA Astrophysics Data System (ADS)

    Tokarev, M. P.; Sharaborin, D. K.; Lobasov, A. S.; Chikishev, L. M.; Dulin, V. M.; Markovich, D. M.

    2015-06-01

    Tomographic particle image velocimetry (PIV) has become a standard tool for 3D velocity measurements in non-reacting flows. However, the majority of the measurements in flows with combustion are limited to small resolved depth compared to the size of the field of view (typically 1 : 10). The limitations are associated with inhomogeneity of the volume illumination and the non-uniform flow seeding, the optical distortions and errors in the 3D calibration, and the unwanted flame luminosity. In the present work, the above constraints were overcome for the tomographic PIV experiment in a laminar axisymmetric premixed flame. The measurements were conducted for a 1 : 1 depth-to-size ratio using a system of eight CCD cameras and a 200 mJ pulsed laser. The results show that camera calibration based on the triangulation of the tracer particles in the non-reacting conditions provided reliable accuracy for the 3D image reconstruction in the flame. The modification of the tomographic reconstruction allowed a posteriori removal of unwanted bright objects, which were located outside of the region of interest but affected the reconstruction quality. This study reports on a novel experience for the instantaneous 3D velocimetry in laboratory-scale flames by using tomographic PIV.

  14. 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.

  15. 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.

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

    PubMed

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

    2013-07-01

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

  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. Sydney-Gunnedah-Bowen Basin deep 3D structure

    NASA Astrophysics Data System (ADS)

    Danis, Cara

    2012-01-01

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

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

    PubMed

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

    2016-07-01

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

  20. 3-D Velocity Model of the Coachella Valley, Southern California Based on Explosive Shots from the Salton Seismic Imaging Project

    NASA Astrophysics Data System (ADS)

    Persaud, P.; Stock, J. M.; Fuis, G. S.; Hole, J. A.; Goldman, M.; Scheirer, D. S.

    2014-12-01

    We have analyzed explosive shot data from the 2011 Salton Seismic Imaging Project (SSIP) across a 2-D seismic array and 5 profiles in the Coachella Valley to produce a 3-D P-wave velocity model that will be used in calculations of strong ground shaking. Accurate maps of seismicity and active faults rely both on detailed geological field mapping and a suitable velocity model to accurately locate earthquakes. Adjoint tomography of an older version of the SCEC 3-D velocity model shows that crustal heterogeneities strongly influence seismic wave propagation from moderate earthquakes (Tape et al., 2010). These authors improve the crustal model and subsequently simulate the details of ground motion at periods of 2 s and longer for hundreds of ray paths. Even with improvements such as the above, the current SCEC velocity model for the Salton Trough does not provide a match of the timing or waveforms of the horizontal S-wave motions, which Wei et al. (2013) interpret as caused by inaccuracies in the shallow velocity structure. They effectively demonstrate that the inclusion of shallow basin structure improves the fit in both travel times and waveforms. Our velocity model benefits from the inclusion of known location and times of a subset of 126 shots detonated over a 3-week period during the SSIP. This results in an improved velocity model particularly in the shallow crust. In addition, one of the main challenges in developing 3-D velocity models is an uneven stations-source distribution. To better overcome this challenge, we also include the first arrival times of the SSIP shots at the more widely spaced Southern California Seismic Network (SCSN) in our inversion, since the layout of the SSIP is complementary to the SCSN. References: Tape, C., et al., 2010, Seismic tomography of the Southern California crust based on spectral-element and adjoint methods: Geophysical Journal International, v. 180, no. 1, p. 433-462. Wei, S., et al., 2013, Complementary slip distributions

  1. Spatial parallelism of a 3D finite difference, velocity-stress elastic wave propagation code

    SciTech Connect

    Minkoff, S.E.

    1999-12-01

    Finite difference methods for solving the wave equation more accurately capture the physics of waves propagating through the earth than asymptotic solution methods. Unfortunately, finite difference simulations for 3D elastic wave propagation are expensive. The authors model waves in a 3D isotropic elastic earth. The wave equation solution consists of three velocity components and six stresses. The partial derivatives are discretized using 2nd-order in time and 4th-order in space staggered finite difference operators. Staggered schemes allow one to obtain additional accuracy (via centered finite differences) without requiring additional storage. The serial code is most unique in its ability to model a number of different types of seismic sources. The parallel implementation uses the MPI library, thus allowing for portability between platforms. Spatial parallelism provides a highly efficient strategy for parallelizing finite difference simulations. In this implementation, one can decompose the global problem domain into one-, two-, and three-dimensional processor decompositions with 3D decompositions generally producing the best parallel speedup. Because I/O is handled largely outside of the time-step loop (the most expensive part of the simulation) the authors have opted for straight-forward broadcast and reduce operations to handle I/O. The majority of the communication in the code consists of passing subdomain face information to neighboring processors for use as ghost cells. When this communication is balanced against computation by allocating subdomains of reasonable size, they observe excellent scaled speedup. Allocating subdomains of size 25 x 25 x 25 on each node, they achieve efficiencies of 94% on 128 processors. Numerical examples for both a layered earth model and a homogeneous medium with a high-velocity blocky inclusion illustrate the accuracy of the parallel code.

  2. Spatial Parallelism of a 3D Finite Difference, Velocity-Stress Elastic Wave Propagation Code

    SciTech Connect

    MINKOFF,SUSAN E.

    1999-12-09

    Finite difference methods for solving the wave equation more accurately capture the physics of waves propagating through the earth than asymptotic solution methods. Unfortunately. finite difference simulations for 3D elastic wave propagation are expensive. We model waves in a 3D isotropic elastic earth. The wave equation solution consists of three velocity components and six stresses. The partial derivatives are discretized using 2nd-order in time and 4th-order in space staggered finite difference operators. Staggered schemes allow one to obtain additional accuracy (via centered finite differences) without requiring additional storage. The serial code is most unique in its ability to model a number of different types of seismic sources. The parallel implementation uses the MP1 library, thus allowing for portability between platforms. Spatial parallelism provides a highly efficient strategy for parallelizing finite difference simulations. In this implementation, one can decompose the global problem domain into one-, two-, and three-dimensional processor decompositions with 3D decompositions generally producing the best parallel speed up. Because i/o is handled largely outside of the time-step loop (the most expensive part of the simulation) we have opted for straight-forward broadcast and reduce operations to handle i/o. The majority of the communication in the code consists of passing subdomain face information to neighboring processors for use as ''ghost cells''. When this communication is balanced against computation by allocating subdomains of reasonable size, we observe excellent scaled speed up. Allocating subdomains of size 25 x 25 x 25 on each node, we achieve efficiencies of 94% on 128 processors. Numerical examples for both a layered earth model and a homogeneous medium with a high-velocity blocky inclusion illustrate the accuracy of the parallel code.

  3. 3D Droplet velocities and sizes in the Ranque-Hilsch vortex tube

    NASA Astrophysics Data System (ADS)

    Liew, R.; Zeegers, J. C. H.; Kuerten, J. G. M.; Michalek, W. R.

    2012-11-01

    The Ranque-Hilsch vortex tube is a known device that is used to generate spot cooling. In this study, we experimentally investigate the behavior of small water droplets in the vortex tube by means of Phase Doppler Particle Analysis. In an experimental vortex tube, droplets were injected together with a carrier gas to form a fast rotating (up to 80.000 rpm) droplet-gas mixture. Droplet sizes, 3D velocity components, and turbulent properties were measured, showing high intensity isotropic turbulence in the core region. To investigate the cause of the high intensity turbulence, a frequency analysis was applied on the measured velocity. The frequency spectrum of the velocity is presented and indicates that wobbling of the vortex axis is the cause of the high turbulence intensity. It was expected that larger droplets have a higher radial velocity because of the larger centrifugal force. Results show, however, that small and lager droplets behave similar. This research is supported by the Dutch Technology Foundation STW, which is the applied science division of NWO, and the Technology Programme of the Ministry of Economic Affairs.

  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 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

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

    PubMed

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

    2015-01-01

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

  7. Using Ambient Noise Data from the ALBACORE OBS Array to Determine a 3D Seismic Velocity Model Offshore Southern California

    NASA Astrophysics Data System (ADS)

    Kohler, M. D.; Bowden, D. C.; Tsai, V. C.; Weeraratne, D. S.

    2014-12-01

    The Pacific-North America plate boundary in Southern California extends far west of the coastline, and a 12-month ocean bottom seismometer (OBS) array spanned the western side of the plate boundary in order to image seismic velocities in the lithosphere. Velocities are modeled through stacked cross correlations of ambient noise data. The offshore data come primarily from the OBS array that collected 12 months of continuous data during 2010-2011, combined with Southern California Seismic Network (SCSN) station data. The cross correlations were stacked for noise correlation functions and examined using standard time- and frequency-domain methods to determine phase velocity and group velocity dispersion curves. Signals between the vertical-component OBS and co-located horizontal-component OBS observations associated with tilt noise, and pressure gauge observations associated with infragravity waves, were examined to further improve signals. The non-elastic noise was estimated by calculating the transfer functions between the vertical-to-horizontal and vertical-to-pressure components, and subtracting the coherent signal between the two from the vertical-component time series. We find that these effects are small in our dataset. We are simultaneously inverting all measureable dispersion curves to solve for 3D crustal velocity structure. Shear-wave velocities comprise the direct solution, and Vp/Vs ratios are constrained as much as the data allow. Calculations on data from 780 OBS-OBS, SCSN-SCSN, and OBS-SCSN pairs filtered around multiple narrow bands between 5 and 50 s show clear propagating waves traveling at group velocities between 1.2 and 3.5 km/s. The longer-term outcome of this work will comprise a 3D crustal and uppermost mantle velocity model with areal coverage not attainable before the deployment of the ocean bottom seismometers. The results define the transition in three dimensions from continental lithospheric structure in the near-shore region to oceanic

  8. Three-Dimensional (3-D) Reconstructions of EISCAT IPS Velocity Data in the Declining Phase of Solar Cycle 23

    NASA Astrophysics Data System (ADS)

    Bisi, M. M.; Jackson, B. V.; Breen, A. R.; Dorrian, G. D.; Fallows, R. A.; Clover, J. M.; Hick, P. P.

    2010-08-01

    The European Incoherent SCATter (EISCAT) radar has been used for remote-sensing observations of interplanetary scintillation (IPS) for a quarter of a century. During the April/May 2007 observing campaign, a large number of observations of IPS using EISCAT took place to give a reasonable spatial and temporal coverage of solar wind velocity structure throughout this time during the declining phase of Solar Cycle 23. Many co-rotating and transient features were observed during this period. Using the University of California, San Diego three-dimensional (3-D) time-dependent computer assisted tomography (C.A.T.) solar-wind reconstruction analysis, we show the velocity structure of the inner heliosphere in three dimensions throughout the time interval of 20 April through 20 May 2007. We also compare to white-light remote-sensing observations of an interplanetary coronal mass ejection (ICME) seen by the STEREO Ahead spacecraft inner Heliospheric Imager on 16 May 2007, as well as to in-situ solar-wind measurements taken with near-Earth spacebourne instrumentation throughout this interval. The reconstructions show clear co-rotating regions during this period, and the time-series extraction at spacecraft locations compares well with measurements made by the STEREO, Wind, and ACE spacecraft. This is the first time such clear structures have been revealed using this 3-D technique with EISCAT IPS data as input.

  9. 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.

  10. Near-wall 3D velocity measurements above biomimetic shark skin denticles using Digital In-line Holographic Microscopy

    NASA Astrophysics Data System (ADS)

    Toloui, Mostafa; Brajkovic, David; Hong, Jiarong

    2014-11-01

    Digital In-line Holography is employed to image 3D flow structures in the vicinity of a transparent rough surface consisting of closely packed biomimetic shark skin denticles as roughness elements. The 3D printed surface replicates the morphological features of real shark skin, and the denticles have a geometrical scale of 2 mm, i.e. 10 times of the real ones. In order to minimize optical aberrations near the fluid-roughness interface and enable flow measurements around denticles, the optical refractive index of the fluid medium is maintained the same as that of the denticle model in an index-matched flow facility using NaI solution as the working fluid. The experiment is conducted in a 1.2 m long test section with 50 mm × 50 mm cross section. The sampling volume is located in the downstream region of a shark skin replica of 12'' stretch where the turbulent flow is fully-developed and the transitional effect from smooth to the rough surface becomes negligible. Several instantaneous realizations of the 3D velocity field are obtained and are used to illustrate turbulent coherent structures induced by shark-skin denticles. This information will provide insights on the hydrodynamic function of shark's unique surface ornamentation.

  11. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  12. 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

  13. 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.

  14. 3D reconstruction methods of coronal structures by radio observations

    NASA Astrophysics Data System (ADS)

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

    1992-11-01

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

  15. 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.

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

    PubMed

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

    2014-09-23

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

  17. 3D precision surface measurement by dynamic structured light

    NASA Astrophysics Data System (ADS)

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

    2004-02-01

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

  18. 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

  19. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

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

    2012-07-01

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

  20. 3-D lookup: Fast protein structure database searches

    SciTech Connect

    Holm. L.; Sander, C.

    1995-12-31

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

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

    PubMed

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

    2012-01-21

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  4. Simultaneous measurement of 3D zooplankton trajectories and surrounding fluid velocity field in complex flows.

    PubMed

    Adhikari, Deepak; Gemmell, Brad J; Hallberg, Michael P; Longmire, Ellen K; Buskey, Edward J

    2015-11-01

    We describe an automated, volumetric particle image velocimetry (PIV) and tracking method that measures time-resolved, 3D zooplankton trajectories and surrounding volumetric fluid velocity fields simultaneously and non-intrusively. The method is demonstrated for groups of copepods flowing past a wall-mounted cylinder. We show that copepods execute escape responses when subjected to a strain rate threshold upstream of a cylinder, but the same threshold range elicits no escape responses in the turbulent wake downstream. The method was also used to document the instantaneous slip velocity of zooplankton and the resulting differences in trajectory between zooplankton and non-inertial fluid particles in the unsteady wake flow, showing the method's capability to quantify drift for both passive and motile organisms in turbulent environments. Applications of the method extend to any group of organisms interacting with the surrounding fluid environment, where organism location, larger-scale eddies and smaller-scale fluid deformation rates can all be tracked and analyzed. PMID:26486364

  5. Coronal Outflow Velocities in a 3D Coronal Model Determined from UVCS Doppler Dimming Observations

    NASA Astrophysics Data System (ADS)

    Strachan, L.; Panasyuk, A. V.; Dobrzycka, D.; Gibson, S.; Biesecker, D. A.; Ko, Y.-K.; Galvin, A. B.; Romoli, M.; Kohn, J. L.

    1998-04-01

    We constrain coronal outflow velocity solutions, resolved along the line-of-sight, by using Doppler dimming models of H I Lyman alpha and O VI 1032/1037 Angstrom emissivities obtained with data from the Ultraviolet Coronagraph Spectrometer (UVCS) on SOHO. The local emissivities, from heliocentric heights of 1.5 to 3.0 radii, were determined from 3-D reconstructions of line-of-sight intensities obtained during the Whole Sun Month Campaign (10 Aug. -- 8 Sep. 1996). The models use electron densities derived from polarized brightness measurements made with the visible light coronagraphs on UVCS and LASCO, supplemented with data from Mark III at NCAR/MLSO. Electron temperature profiles are derived from `freezing-in' temperatures obtained from an analysis of charge state data from SWICS/Ulysses. The work concentrates on O5+ outflow velocities which are determined from an analysis of the the O VI line ratios. This analysis is less sensitive to the uncertainties in the electron density and independent of the ionization balance and elemental abundance than the analyses which use individual spectral lines. This work is supported in part by NASA under grant NAG-3192 to the Smithsonian Astrophysical Observatory, by the Italian Space Agency and by Swiss funding agencies.

  6. 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.

  7. Using Adjoint Methods to Improve 3-D Velocity Models of Southern California

    NASA Astrophysics Data System (ADS)

    Liu, Q.; Tape, C.; Maggi, A.; Tromp, J.

    2006-12-01

    We use adjoint methods popular in climate and ocean dynamics to calculate Fréchet derivatives for tomographic inversions in southern California. The Fréchet derivative of an objective function χ(m), where m denotes the Earth model, may be written in the generic form δχ=int Km(x) δln m(x) d3x, where δln m=δ m/m denotes the relative model perturbation. For illustrative purposes, we construct the 3-D finite-frequency banana-doughnut kernel Km, corresponding to the misfit of a single traveltime measurement, by simultaneously computing the 'adjoint' wave field s† forward in time and reconstructing the regular wave field s backward in time. The adjoint wave field is produced by using the time-reversed velocity at the receiver as a fictitious source, while the regular wave field is reconstructed on the fly by propagating the last frame of the wave field saved by a previous forward simulation backward in time. The approach is based upon the spectral-element method, and only two simulations are needed to produce density, shear-wave, and compressional-wave sensitivity kernels. This method is applied to the SCEC southern California velocity model. Various density, shear-wave, and compressional-wave sensitivity kernels are presented for different phases in the seismograms. We also generate 'event' kernels for Pnl, S and surface waves, which are the Fréchet kernels of misfit functions that measure the P, S or surface wave traveltime residuals at all the receivers simultaneously for one particular event. Effectively, an event kernel is a sum of weighted Fréchet kernels, with weights determined by the associated traveltime anomalies. By the nature of the 3-D simulation, every event kernel is also computed based upon just two simulations, i.e., its construction costs the same amount of computation time as an individual banana-doughnut kernel. One can think of the sum of the event kernels for all available earthquakes, called the 'misfit' kernel, as a graphical

  8. 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.

  9. 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.

  10. A 3D Seismic Velocity Model Offshore Southern California from Ambient Noise Tomography of the ALBACORE OBS Array

    NASA Astrophysics Data System (ADS)

    Kohler, M. D.; Bowden, D. C.; Tsai, V. C.; Weeraratne, D. S.

    2015-12-01

    The Pacific-North America plate boundary in Southern California extends far west of the coastline, and a 12-month ocean bottom seismometer (OBS) array spanned the western side of the plate boundary to image lithospheric seismic velocities. Velocities are modeled through stacked cross correlations of ambient noise data. Twelve months of continuous data were used from 22 OBS stations and ~30 coastal and island Southern California Seismic Network stations. Particular attention has been paid to improving signal-to-noise ratios in the noise correlations with OBS stations by removing the effects of instrument tilt and infragravity waves. Different applications of preprocessing techniques allow us to distinguish the fundamental and first higher order Rayleigh modes, especially in deep water OBS pairs where the water layer dominates crustal sensitivity of the fundamental mode. Standard time domain and frequency domain methods are used to examine surface wave dispersion curves for group and phase velocities between 5 and 50 second periods, and these are inverted for 3D velocity structure. The results define the transition in three dimensions from continental lithospheric structure in the near-shore region to oceanic structure west of the continental borderland. While the most prominent features of the model relate to thinning of the crust west of the Patton Escarpment, other notable anomalies are present north-to-south throughout the continental borderland and along the coast from the Los Angeles Basin to the Peninsular Ranges. The velocity model will help describe the region's tectonic history, as well as provide new constraints for determination of earthquake relocations and rupture styles.

  11. Engineering extracellular matrix structure in 3D multiphase tissues

    PubMed Central

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

    2011-01-01

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

  12. 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.

  13. 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 area of Poland a contact between the Precambrian and Phanerozoic Europe and the Carpathians has a complicated structure and a complex P-wave velocity of the sedimentary cover, crystalline crust, Moho depth and the uppermost mantle. The geometry of the uppermost several kilometers of sediments is relatively well recognized from over 100,000 boreholes. The vertical seismic profiling (VSP) from 1188 boreholes provided detailed velocity data for regional tectonic units and for stratigraphic successions from Permian to the Tertiary and Quaternary deposits. These data, however, do not provide information about the velocity and basement depth in the central part of the Trans-European suture zone (TESZ) and in the Carpathians. So, the data set is supplemented by 2D velocity models from 32 deep seismic sounding refraction profiles which also provide information about the crust and uppermost mantle. Together with the results of other methods: vertical seismic profiling, magnetotelluric, allow for the creation of a detailed, high-resolution 3D model for the entire Earth's crust and the uppermost mantle down to a depth of 60 km. The thinnest sedimentary cover in the Mazury-Belarus anteclise is only 0.3 to 1 km thick, which increases to 7 to 8 km along the East European Craton (EEC) margin, and 9 to 12 km in the TESZ. The Variscan domain is characterized by a 1-4 km thick sedimentary cover, while the Carpathians are characterized by very thick sedimentary layers, up to about 20 km. The crystalline crust is differentiated and has a layered structure. The crust beneath the West European Platform (WEP; Variscan domain) is characterized by P-wave velocities of 5.8-6.6 km/s. The upper and middle crusts beneath the EEC are characterized by velocities of 6.1-6.6 km/s, and are underlain by a high velocity lower crust with a velocity of about 7 km/s. A general decrease in velocity is observed from the older to the younger tectonic domains. The TESZ is associated with a steep dip

  14. SALSA3D: Validating a Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location

    NASA Astrophysics Data System (ADS)

    Begnaud, M. L.; Ballard, S.; Young, C. J.; Hipp, J. R.; Encarnacao, A.; Phillips, W. S.; Chael, E. P.; Rowe, C. A.

    2012-12-01

    We are developing a global 3D P wave velocity model of the Earth's crust and mantle using seismic tomography to assess improvement to seismic event locations obtained using high quality 3D Earth models in lieu of 1D and 2/2.5D models. We present the most recent version of SALSA3D (SAndia LoS Alamos 3D) version 1.9, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth (GT) events. Our model is derived from the latest version of the GT catalog of P/Pn travel-time picks assembled by Los Alamos National Laboratory. For this current version, we employ more robust data quality control measures than previously used, as well as additional global GT data sources. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays into representative rays. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions. For our starting model, we use a simplified layer crustal model derived from the NNSA Unified model in Eurasia and Crust 2.0 model everywhere else, overlying a uniform ak135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changes between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only in areas where the data warrant such a refinement. In previous versions, we based this refinement on velocity changes from previous model iterations. For the current version, we utilize the diagonal of the model resolution matrix to control where grid refinement occurs, resulting in more consistent and continuous areas of refinement than before. In addition to the changes in grid refinement, we also employ a more robust convergence criterion between successive grid refinements, allowing a better fit to first broader

  15. 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

  16. 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.

  17. 3D Anisotropic Velocity Tomography of a Water Saturated Rock under True-Triaxial Stress in the Laboratory

    NASA Astrophysics Data System (ADS)

    Ghofrani Tabari, M.; Goodfellow, S. D.; Nasseri, M. B.; Young, R.

    2013-12-01

    A cubic specimen of water saturated Fontainebleau Sandstone is tested in the laboratory under true-triaxial loading where three different principal stresses are applied under drained conditions. Due to the loading arrangement, closure and opening of the pre-existing cracks in the rock, as well as creation and growth of the aligned cracks cause elliptical anisotropy and distributed heterogeneities. A Geophysical Imaging Cell equipped with an Acoustic Emission monitoring system is employed to image velocity structure of the sample during the experiment through repeated transducer to transducer non-destructive ultrasonic surveys. Apparent P-wave velocities along the rock body are calculated in different directions and shown in stereonet plots which demonstrate an overall anisotropy of the sample. The apparent velocities in the main three orthogonal cubic directions are used as raw data for building a mean spatial distribution model of anisotropy ratios. This approach is based on the concept of semi-principal axes in an elliptical anisotropic model and appointing two ratios between the three orthogonal velocities in each of the cubic grid cells. The spatial distribution model of anisotropy ratios are used to calculate the anisotropic ray-path segment matrix elements (Gij). These contain segment lengths of the ith ray in the jth cell in three dimensions where, length of each ray in each cell is computed for one principal direction based on the dip and strike of the ray and these lengths differ from the ones in an isotropic G Matrix. 3D strain of the squeezed rock and the consequent geometrical deformation is also included in the ray-path segment matrix. A Singular Value Decomposition (SVD) method is used for inversion from the data space of apparent velocities to the model space of P-wave propagation velocities in the three principal directions. Finally, spatial variation and temporal evolution of induced damages in the rock, representing uniformly distributed or

  18. 3-D velocity heterogeneity in earthquake swarm area of NW Bohemia/Vogtland (German-Czech border region)

    NASA Astrophysics Data System (ADS)

    Mousavi, Sima; Bauer, Klaus; Korn, Michael

    2014-05-01

    3-D Vp and Vp/Vs structure of the geodynamically active NW Bohemia/Vogtland area, located at the border region between Germany and Czech republic, has been determined from local earthquake tomography using 543 earthquakes which have been recorded during 2000 to 2010. This region is known for the occurrence of earthquake swarms that are supposed to be triggered by fluid upwelling in the crust, although fluid behaviour and migration paths in the subsurface of NW Bohemia is still poorly known. The events used in this study were selected based on a minimum 12 P and S phase observations and an azimuthal gap less than 160º. This data set is employed to derive a minimum 1-D velocity model and to relocate the hypocenters. The minimum 1-D velocity model is then used as an initial model in non-linear inversion to derive 3-D P-velocity and Vp/Vs ratio. Using synthetic tests, it can be shown that a high resolution is obtained in the central part of the studied region with the given source and receiver configuration. Two branches of high Vp/Vs ratio anomalies have been detected above the swarm quakes' focal zone. These anomalies support the existence of two main fluid passages toward Bad Brambach and Bublak moffette. Another interesting result is a high Vp/Vs line-like anomaly along Mariánské Lázně fault where most of the swarm quakes occur, which could be due to a fluid saturated area around the cracked zone of the fault plain. Hypocenters in the swarm region are located in a low Vp and Vp/Vs anomaly. The correlation between the detected Vp and Vp/Vs anomalies and the location of earthquake swarm suggests a model in which CO2 as part of magmatic fluids exist in a vast area beneath NW Bohemia and frequently migrate up to the surface.

  19. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

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

    2011-01-01

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

  20. SALSA3D - Improving Event Locations Using a Global 3D P-Velocity Model of the Earth's Crust and Mantle

    NASA Astrophysics Data System (ADS)

    Begnaud, M. L.; Ballard, S.; Young, C. J.; Hipp, J. R.; Chang, M.; Encarnacao, A.; Rowe, C. A.; Phillips, W. S.; Steck, L.

    2011-12-01

    To test the hypothesis that high quality 3D Earth models will produce seismic event locations that are more accurate and more precise than currently used 1D and 2/2.5D models, we are developing a global 3D P wave velocity model of the Earth's crust and mantle using seismic tomography. In this paper, we present the most recent version of our model, SALSA3D (SAndia LoS Alamos 3D) version 1.7, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth (GT) events, compared to existing models and/or systems. Our model is derived from the latest version of the GT catalog of P and Pn travel time picks assembled by Los Alamos National Laboratory. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays to produce representative rays. Reduction in the total number of ray paths is ~50%. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions. For our starting model, we use a simplified layer crustal model derived from the NNSA Unified model in Eurasia and Crust 2.0 model elsewhere, over a uniform ak135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changes between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only in areas where the data warrant it. In previous versions of SALSA3D, we based this refinement on velocity changes from previous model iterations. For version 1.7, we utilize the diagonal of the model resolution matrix to control where grid refinement occurs, resulting in more consistent and continuous areas of refinement than before. Our approach produces a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. We

  1. Energy cost and body centre of mass' 3D intracycle velocity variation in swimming.

    PubMed

    Figueiredo, Pedro; Barbosa, Tiago M; Vilas-Boas, João Paulo; Fernandes, Ricardo J

    2012-09-01

    The purpose of this study was to examine the relationship between the energy cost (C) and the 3D intracycle velocity variation (IVV; swimming direction--x, vertical--y and lateral--z axes) throughout the 200 m front crawl event. Ten international level swimmers performed a maximal 200 m front crawl swim followed by 50, 100 and 150 m bouts at the same pace as in the 200 m splits. Oxygen consumption was measured during the bouts and blood samples were collected before and after each one. The C was calculated for each 50 m lap as the ratio of the total energy expenditure (three energy pathways) to the distance. A respiratory snorkel and valve system with low hydrodynamic resistance was used to measure pulmonary ventilation and to collect breathing air samples. Two above water and four underwater cameras videotaped the swim bouts and thereafter APAS was used to assess the centre of mass IVV (x, y and z components). The increase in the C was significantly associated with the increase in the IVV in x for the first 50 m lap (R = -0.83, P < 0.01). It is concluded that the IVV relationship with C in a competitive event does not present the direct relationship found in the literature, revealing a great specificity, which suggests that the relation between these two parameters could not be used as a performance predictor in competitive events. PMID:22262010

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

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Yelkenci, Seda; Aktar, Mustafa

    2013-04-01

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

  5. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

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

    2016-07-01

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

  6. Experimental Investigation of the Near Wall Flow Structure of a Low Reynolds Number 3-D Turbulent Boundary Layer

    NASA Technical Reports Server (NTRS)

    Fleming, J. L.; Simpson, R. L.

    1997-01-01

    Laser Doppler velocimetry (LDV) measurements and hydrogen bubble flow visualization techniques were used to examine the near-wall flow structure of 2D and 3D turbulent boundary layers (TBLs) over a range of low Reynolds numbers. The goals of this research were (1) an increased understanding of the flow physics in the near wall region of turbulent boundary layers,(2) to observe and quantify differences between 2D and 3D TBL flow structures, and (3) to document Reynolds number effects for 3D TBLs. The LDV data have provided results detailing the turbulence structure of the 2D and 3D TBLs. These results include mean Reynolds stress distributions, flow skewing results, and U and V spectra. Effects of Reynolds number for the 3D flow were also examined. Comparison to results with the same 3D flow geometry but at a significantly higher Reynolds number provided unique insight into the structure of 3D TBLs. While the 3D mean and fluctuating velocities were found to be highly dependent on Reynolds number, a previously defined shear stress parameter was discovered to be invariant with Reynolds number. The hydrogen bubble technique was used as a flow visualization tool to examine the near-wall flow structure of 2D and 3D TBLs. Both the quantitative and qualitative results displayed larger turbulent fluctuations with more highly concentrated vorticity regions for the 2D flow.

  7. A hybrid experimental-numerical technique for determining 3D velocity fields from planar 2D PIV data

    NASA Astrophysics Data System (ADS)

    Eden, A.; Sigurdson, M.; Mezić, I.; Meinhart, C. D.

    2016-09-01

    Knowledge of 3D, three component velocity fields is central to the understanding and development of effective microfluidic devices for lab-on-chip mixing applications. In this paper we present a hybrid experimental-numerical method for the generation of 3D flow information from 2D particle image velocimetry (PIV) experimental data and finite element simulations of an alternating current electrothermal (ACET) micromixer. A numerical least-squares optimization algorithm is applied to a theory-based 3D multiphysics simulation in conjunction with 2D PIV data to generate an improved estimation of the steady state velocity field. This 3D velocity field can be used to assess mixing phenomena more accurately than would be possible through simulation alone. Our technique can also be used to estimate uncertain quantities in experimental situations by fitting the gathered field data to a simulated physical model. The optimization algorithm reduced the root-mean-squared difference between the experimental and simulated velocity fields in the target region by more than a factor of 4, resulting in an average error less than 12% of the average velocity magnitude.

  8. 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.

  9. SALSA3D - A Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location

    NASA Astrophysics Data System (ADS)

    Ballard, S.; Begnaud, M. L.; Young, C. J.; Hipp, J. R.; Chang, M.; Encarnacao, A. V.; Rowe, C. A.; Phillips, W. S.; Steck, L.

    2010-12-01

    To test the hypothesis that high quality 3D Earth models will produce seismic event locations which are more accurate and more precise, we are developing a global 3D P wave velocity model of the Earth’s crust and mantle using seismic tomography. In this paper, we present the most recent version of our model, SALSA3D version 1.5, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth events. Our model is derived from the latest version of the Ground Truth (GT) catalog of P and Pn travel time picks assembled by Los Alamos National Laboratory. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays to produce representative rays. Reduction in the total number of ray paths is ~50%. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions.. For our starting model, we use a simplified two layer crustal model derived from the Crust 2.0 model over a uniform AK135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changes between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only around areas with significant velocity changes from the starting model. At each grid refinement level except the last one we limit the number of iterations to prevent convergence thereby preserving aspects of broad features resolved at coarser resolutions. Our approach produces a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. This scheme is computationally expensive, so we use a distributed computing framework based on the Java Parallel Processing Framework, providing us with ~400 processors. Resolution of our model is assessed using a

  10. Analysis of non linear partially standing waves from 3D velocity measurements

    NASA Astrophysics Data System (ADS)

    Drevard, D.; Rey, V.; Svendsen, Ib; Fraunie, P.

    2003-04-01

    Surface gravity waves in the ocean exhibit an energy spectrum distributed in both frequency and direction of propagation. Wave data collection is of great importance in coastal zones for engineering and scientific studies. In particular, partially standing waves measurements near coastal structures and steep or barred beaches may be a requirement, for instance for morphodynamic studies. The aim of the present study is the analysis of partially standing surface waves icluding non-linear effects. According to 1st order Stokes theory, synchronous measurements of horizontal and vertical velocity components allow calculation of rate of standing waves (Drevard et al, 2003). In the present study, it is demonstrated that for deep water conditions, partially standing 2nd order Stokes waves induced velocity field is still represented by the 1st order solution for the velocity potential contrary to the surface elevation which exhibits harmonic components. For intermediate water depth, harmonic components appear not only in the surface elevation but also in the velocity fields, but their weight remains much smaller, because of the vertical decreasing wave induced motion. For irregular waves, the influence of the spectrum width on the non-linear effects in the analysis is discussed. Keywords: Wave measurements ; reflection ; non-linear effects Acknowledgements: This work was initiated during the stay of Prof. Ib Svendsen, as invited Professor, at LSEET in autumn 2002. This study is carried out in the framework of the Scientific French National Programmes PNEC ART7 and PATOM. Their financial supports are acknowledged References: Drevard, D., Meuret, A., Rey, V. Piazzola, J. And Dolle, A.. (2002). "Partially reflected waves measurements using Acoustic Doppler Velocimeter (ADV)", Submitted to ISOPE 03, Honolulu, Hawaii, May 2003.

  11. 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.

  12. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

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

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

    PubMed

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

    2014-07-01

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

  14. Application of Plenoptic PIV for 3D Velocity Measurements Over Roughness Elements in a Refractive Index Matched Facility

    NASA Astrophysics Data System (ADS)

    Thurow, Brian; Johnson, Kyle; Kim, Taehoon; Blois, Gianluca; Best, Jim; Christensen, Ken

    2014-11-01

    The application of Plenoptic PIV in a Refractive Index Matched (RIM) facility housed at Illinois is presented. Plenoptic PIV is an emerging 3D diagnostic that exploits the light-field imaging capabilities of a plenoptic camera. Plenoptic cameras utilize a microlens array to measure the position and angle of light rays captured by the camera. 3D/3C velocity fields are determined through application of the MART algorithm for volume reconstruction and a conventional 3D cross-correlation PIV algorithm. The RIM facility is a recirculating tunnel with a 62.5% aqueous solution of sodium iodide used as the working fluid. Its resulting index of 1.49 is equal to that of acrylic. Plenoptic PIV was used to measure the 3D velocity field of a turbulent boundary layer flow over a smooth wall, a single wall-mounted hemisphere and a full array of hemispheres (i.e. a rough wall) with a k/ δ ~ 4.6. Preliminary time averaged and instantaneous 3D velocity fields will be presented. This material is based upon work supported by the National Science Foundation under Grant No. 1235726.

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

    NASA Astrophysics Data System (ADS)

    Polkowski, Marcin; Grad, Marek

    2015-04-01

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

  16. Zemmouri earthquake rupture zone (Mw 6.8, Algeria): Aftershocks sequence relocation and 3D velocity model

    NASA Astrophysics Data System (ADS)

    Ayadi, A.; Dorbath, C.; Ousadou, F.; Maouche, S.; Chikh, M.; Bounif, M. A.; Meghraoui, M.

    2008-09-01

    We analyze the aftershocks sequence of the Zemmouri thrust faulting earthquake (21 May 2003, Mw 6.8) located east of Algiers in the Tell Atlas. The seismic sequence located during ˜2 months following the mainshock is made of more than 1500 earthquakes and extends NE-SW along a ˜60-km fault rupture zone crossing the coastline. The earthquake relocation was performed using handpicked P and S phases located with the tomoDD in a detailed 3D velocity structure of the epicentral area. Contrasts between velocity patches seem to correlate with contacts between granitic-volcanic basement rocks and the sedimentary formation of the eastern Mitidja basin. The aftershock sequence exhibits at least three seismic clouds and a well-defined SE-dipping main fault geometry that reflects the complex rupture. The distribution of seismic events presents a clear contrast between a dense SW zone and a NE zone with scattered aftershocks. We observe that the mainshock locates between the SW and NE seismic zones; it also lies at the NNS-SSE contact that separates a basement block to the east and sedimentary formations to the west. The aftershock distribution also suggests fault bifurcation at the SW end of the fault rupture, with a 20-km-long ˜N 100° trending seismic cluster, with a vertical fault geometry parallel to the coastline juxtaposed. Another aftershock cloud may correspond to 75° SE dipping fault. The fault geometry and related SW branches may illustrate the interference between pre-existing fault structures and the SW rupture propagation. The rupture zone, related kinematics, and velocity contrasts obtained from the aftershocks distribution are in agreement with the coastal uplift and reflect the characteristics of an active zone controlled by convergent movements at a plate boundary.

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

    PubMed Central

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

    2014-01-01

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

  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. 3D Velocity and Hypocentre Distribution About a Cone-Volcano: Mt Taranaki, New Zealand

    NASA Astrophysics Data System (ADS)

    Sherburn, S.; White, R.

    2003-12-01

    Mt Taranaki is a 2518 m andesite cone-volcano (last eruption AD1755) within an oil-bearing sedimentary basin approximately 50 km west of the deepest part of the Benioff zone beneath the North Island of New Zealand. It is the most recent of a series of volcanoes that have erupted in the Taranaki region in the last 1.7 million years. Although a permanent six-station seismic network monitors Mt Taranaki for signs of unrest, little is known of the structure at the depths earthquakes occur and magma maybe stored. This information is vital for interpreting precursors to any future eruption. For nine months in 2001-2002, a temporary network of 75 three-component, broadband (0.03 - 50 Hz) seismographs (area c. 100 km by 100 km) was used to collect data to image crustal structure and accurately locate earthquakes in the Taranaki region. Three hundred and eighty-nine earthquakes were located using more than 15,000 phase picks (55% P and 45% S). A joint inversion for 1D Vp, Vs and hypocentres was undertaken using Velest followed by a 3D inversion for Vp, Vp/Vs ratio and hypocentres using Simul2000. The base of the seismogenic zone increases gradually from a depth of 20 km immediately west of Mt Taranaki to 35 km deep 100 km to the east, corresponding to a previously observed increase in crustal thickness. The area close to Mt Taranaki is anomalous in that there are few earthquakes and all are shallower than 10 km. Within the upper 5-10 km of the crust Vp is closely related to surface geology, being high beneath Mt Taranaki, low beneath the surrounding sedimentary basin, and very high to the east of the basin. We present the Vp and Vp/Vs structure and hypocentre distribution of the Taranaki region and discuss features that can be attributed to volcanism at Mt Taranaki and older volcanic centres.

  20. Retrieving 3D Velocity Fields of Glaciers from X-band SAR Data and Comparison with GPS Observations

    NASA Astrophysics Data System (ADS)

    Magnússon, E.; Nagler, T.; Hetzenecker, M.; Palsson, F.; Scharrer, K.; Floricioiu, D.; Berthier, E.; Gudmundsson, S.; Rott, H.

    2013-12-01

    We present 3D velocity fields obtained from time series of TerraSAR-X and TanDEM-X images acquired over the ablation area of the Breidamerkurjökull outlet glacier of Vatnjökull Ice Cap (Iceland) in 2008-2012. Coherent and incoherent offset tracking is applied to repeat pass X-Band data to obtain ice displacement in cross and along track direction. Three methods are tested and compared to extract fields of the 3D ice velocity. First, the conventional surface parallel approach, which we consider as an approximation for deriving the horizontal motion rate, but does not reveal a realistic vertical motion. Second, the combination of offset tracking results from almost simultaneous observations from ascending and descending orbits measuring the glacier motion in four different directions, allowing calculation of the 3D velocity fields without any additional approximations. Third, deriving full 3D velocity fields by using the horizontal flow direction, derived from the ascending-descending combination, as constrain on offset tracking results from a single pair of SAR images. The latter two methods reveal a measurement of the vertical ice motion plus ablation, hence equivalent to the vertical motion component measured by GPS station fixed on a platform laying on the ice surface. The results from all methods are compared with such GPS measurements recorded by permanent stations on the glacier in 2008-2012 and the errors of the different methods are calculated. Additionally, we approximate the contribution of these 3D flow fields to elevation changes (emergence/submergence velocity plus net balance) and compare it with elevation changes from surface DEMs obtained in 2008 (SPIRIT), 2010 (airborne LIDAR) and 2012 (TanDEM-X).

  1. Seismicity patterns along the Ecuadorian subduction zone: new constraints from earthquake location in a 3-D a priori velocity model

    NASA Astrophysics Data System (ADS)

    Font, Yvonne; Segovia, Monica; Vaca, Sandro; Theunissen, Thomas

    2013-04-01

    To improve earthquake location, we create a 3-D a priori P-wave velocity model (3-DVM) that approximates the large velocity variations of the Ecuadorian subduction system. The 3-DVM is constructed from the integration of geophysical and geological data that depend on the structural geometry and velocity properties of the crust and the upper mantle. In addition, specific station selection is carried out to compensate for the high station density on the Andean Chain. 3-D synthetic experiments are then designed to evaluate the network capacity to recover the event position using only P arrivals and the MAXI technique. Three synthetic earthquake location experiments are proposed: (1) noise-free and (2) noisy arrivals used in the 3-DVM, and (3) noise-free arrivals used in a 1-DVM. Synthetic results indicate that, under the best conditions (exact arrival data set and 3-DVM), the spatiotemporal configuration of the Ecuadorian network can accurately locate 70 per cent of events in the frontal part of the subduction zone (average azimuthal gap is 289° ± 44°). Noisy P arrivals (up to ± 0.3 s) can accurately located 50 per cent of earthquakes. Processing earthquake location within a 1-DVM almost never allows accurate hypocentre position for offshore earthquakes (15 per cent), which highlights the role of using a 3-DVM in subduction zone. For the application to real data, the seismicity distribution from the 3-D-MAXI catalogue is also compared to the determinations obtained in a 1-D-layered VM. In addition to good-quality location uncertainties, the clustering and the depth distribution confirm the 3-D-MAXI catalogue reliability. The pattern of the seismicity distribution (a 13 yr record during the inter-seismic period of the seismic cycle) is compared to the pattern of rupture zone and asperity of the Mw = 7.9 1942 and the Mw = 7.7 1958 events (the Mw = 8.8 1906 asperity patch is not defined). We observe that the nucleation of 1942, 1958 and 1906 events coincides with

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. Microseismic monitoring of soft-rock landslide: contribution of a 3D velocity model for the location of seismic sources.

    NASA Astrophysics Data System (ADS)

    Floriane, Provost; Jean-Philippe, Malet; Cécile, Doubre; Julien, Gance; Alessia, Maggi; Agnès, Helmstetter

    2015-04-01

    Characterizing the micro-seismic activity of landslides is an important parameter for a better understanding of the physical processes controlling landslide behaviour. However, the location of the seismic sources on landslides is a challenging task mostly because of (a) the recording system geometry, (b) the lack of clear P-wave arrivals and clear wave differentiation, (c) the heterogeneous velocities of the ground. The objective of this work is therefore to test whether the integration of a 3D velocity model in probabilistic seismic source location codes improves the quality of the determination especially in depth. We studied the clay-rich landslide of Super-Sauze (French Alps). Most of the seismic events (rockfalls, slidequakes, tremors...) are generated in the upper part of the landslide near the main scarp. The seismic recording system is composed of two antennas with four vertical seismometers each located on the east and west sides of the seismically active part of the landslide. A refraction seismic campaign was conducted in August 2014 and a 3D P-wave model has been estimated using the Quasi-Newton tomography inversion algorithm. The shots of the seismic campaign are used as calibration shots to test the performance of the different location methods and to further update the 3D velocity model. Natural seismic events are detected with a semi-automatic technique using a frequency threshold. The first arrivals are picked using a kurtosis-based method and compared to the manual picking. Several location methods were finally tested. We compared a non-linear probabilistic method coupled with the 3D P-wave model and a beam-forming method inverted for an apparent velocity. We found that the Quasi-Newton tomography inversion algorithm provides results coherent with the original underlaying topography. The velocity ranges from 500 m.s-1 at the surface to 3000 m.s-1 in the bedrock. For the majority of the calibration shots, the use of a 3D velocity model

  7. Micro-CT for the quantification of 3D voids within damaged structures

    SciTech Connect

    Patterson, Brian M; Hamilton, Christopher E; Cerreta, Ellen K; Dennis - Koller, Darcie; Bronkhorst, C. A.; Hansen, B. L.

    2011-01-26

    Micro X-ray Computed Tomography (MXCT) is widely used in the materials community to examine the internal structure of materials for voids and cracks due to damage or casting, or other defects. Most research in this area focuses on the qualitative aspect of the image, simply answering; Are there voids present? Here we present an ongoing study of the quantified incipient spall voids in Cu with different grain sizes, using a gas gun with various velocities. Data analysis packages for MXCT are just now becoming able to dimensionally measure and produce statistics on the voids-present. In order to make the size of the features in the 3D image quantifiable, the question, how many radiographs are required to render the object dimensionally accurate in 3D, must be answered. A series of data sets has been coUected, varying the number of radiographs collected in order to determine the appropriate number required.

  8. Transition zone structure beneath NE China from 3D waveform modelling: Subduction related plumes

    NASA Astrophysics Data System (ADS)

    Tang, Y.; Grand, S. P.; Niu, F.

    2013-12-01

    Seismic tomography is currently used to image deep structure on global and local scales. However, tomography inversions usually underestimate amplitudes and likely cannot resolve narrow slow anomalies in the deep mantle. Careful modelling of waveform distortions has the potential to provide better constraints on small scale anomalies in the mantle. We observed strong waveform distortions from several earthquakes that propagated through a low velocity anomaly in the mantle transition zone beneath the Changbaishan volcanic center, Northeast China. The slow anomaly was recently found by tomography results using the NECESSArray. For each earthquake, there exists a cluster of stations whose S-wave amplitude is substantially higher than the other stations. Also, at the stations near the edges of the cluster, the recorded S waves become more complex, usually featuring two pulses with smaller amplitude. We used the spectral-element method (SPECFEM3D) to construct 3D waveforms using the tomographic model as a starting input model. Synthetic modeling indicated that the observed large amplitude and double arrivals for each cluster can be explained by a strong low velocity anomaly with a diameter of ~200 km surrounded by high velocities in the transition zone. The velocity contrast between the slow anomaly and the surrounding medium is at least 8%, which is double that found in the original tomographic model. The large velocity contrast (8%) cannot be the velocity contrast between the slab and normal transition zone mantle because if this were the case a travel time misfit with observed data to the west would result in. We speculate that the slow anomaly is a manifestation of a return flow upwelling through a slab gap in the mantle transition zone that feeds Changbaishan volcanism. The upwelling mantle is likely hot, and the heat source may come from warm, buoyant sub-lithospheric mantle entrained with the sinking lithosphere that requires an opening to rise.

  9. Segment-interaction in sprint start: Analysis of 3D angular velocity and kinetic energy in elite sprinters.

    PubMed

    Slawinski, J; Bonnefoy, A; Ontanon, G; Leveque, J M; Miller, C; Riquet, A; Chèze, L; Dumas, R

    2010-05-28

    The aim of the present study was to measure during a sprint start the joint angular velocity and the kinetic energy of the different segments in elite sprinters. This was performed using a 3D kinematic analysis of the whole body. Eight elite sprinters (10.30+/-0.14s 100 m time), equipped with 63 passive reflective markers, realised four maximal 10 m sprints start on an indoor track. An opto-electronic Motion Analysis system consisting of 12 digital cameras (250 Hz) was used to collect the 3D marker trajectories. During the pushing phase on the blocks, the 3D angular velocity vector and its norm were calculated for each joint. The kinetic energy of 16 segments of the lower and upper limbs and of the total body was calculated. The 3D kinematic analysis of the whole body demonstrated that joints such as shoulders, thoracic or hips did not reach their maximal angular velocity with a movement of flexion-extension, but with a combination of flexion-extension, abduction-adduction and internal-external rotation. The maximal kinetic energy of the total body was reached before clearing block (respectively, 537+/-59.3 J vs. 514.9+/-66.0 J; p< or =0.01). These results suggested that a better synchronization between the upper and lower limbs could increase the efficiency of pushing phase on the blocks. Besides, to understand low interindividual variances in the sprint start performance in elite athletes, a 3D complete body kinematic analysis shall be used. PMID:20226465

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Muench, Thomas; Koch, Manfred; Schlittenhardt, Jörg

    2010-05-01

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

  12. On the critical one-component velocity regularity criteria to 3-D incompressible MHD system

    NASA Astrophysics Data System (ADS)

    Liu, Yanlin

    2016-05-01

    Let (u , b) be a smooth enough solution of 3-D incompressible MHD system. We prove that if (u , b) blows up at a finite time T*, then for any p ∈ ] 4 , ∞ [, there holds ∫0T* (‖u3(t‧) ‖ H ˙ 1/2 +2/p p + ‖b(t‧) ‖ H ˙ 1/2 +2/p p) dt‧ = ∞. We remark that all these quantities are in the critical regularity of the MHD system.

  13. Effect of catheter placement on 3-D velocity profiles in curved tubes resembling the human coronary system.

    PubMed

    Krams, R; Wentzel, J J; Cespedes, I; Vinke, R; Carlier, S; van der Steen, A F; Lancee, C T; Slager, C J

    1999-06-01

    Novel measurement techniques based on intravenous ultrasound (IVUS) technology ('IVUS-Flowmetry') require the location of a catheter inside the coronary bed. The present study quantifies disturbances in the 3-D velocity profile induced by catheter placement inside a tube, applying computational fluid dynamics. Two curved, circular meshes (radius K = 0.025 m and K = 0.035 m) with and without a catheter inside the lumen were applied. The catheter was located at the inner curve, the outer curve and at the top position. Boundary conditions were: no slip on the wall, zero stress at the outlet, uniform inflow with entrance velocities of 0.1, 0.2 and 0.4 m/s. Curvature-associated centrifugal forces shifted the maximal velocity to the outer curve and introduced two symmetrical vortices. Additional catheter placement redistributed the 3-D axial velocity field away from the catheter, which was accompanied by the appearance of multiple low-strength vortices. In addition, peak axial velocity increased, peak secondary velocities decreased, axial pressure drop increased and shear stress increased. Flow calculations simulated to resemble IVUS-based flowmetry changed by only 1% after considering secondary velocity. In conclusion, placement of a catheter inside a curved tube resembling the human coronary system changes the velocity field and reduces secondary patterns. The present study supports the usefulness of catheter-based flowmetry during resting flow conditions. During hyperemic flow conditions, flow measurements might be accompanied by large axial pressure drops because the catheter, itself, might act as a significant stenosis. PMID:10414897

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

    PubMed

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

    2015-12-01

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

  15. Poloidal structure of the plasma edge with 3D magnetic fields

    NASA Astrophysics Data System (ADS)

    Agostini, Matteo; Scarin, Paolo; Carraro, Lorella; Spizzo, Gianluca; Spolaore, Monica; Vianello, Nicola

    2015-11-01

    In the RFX-mod reversed-field pinch, when the magnetic field spontaneously develops a non axi-symmetric structure, also the plasma edge assumes a three dimensional shape. In previous RFX works, it has been shown that kinetic properties of the plasma (electron pressure, connection lengths, floating potential, influx, plasma flow) closely follow the symmetry of the 3D field, both in amplitude and phase, along the toroidal angle (i.e, the RFP perpendicular direction in the edge). Using a set of poloidally distributed diagnostics, it is shown that these same properties follow the poloidal periodicity (m =1) of the field. However, the behavior of the phase is more difficult to understand. In particular, the 3D modulation of the plasma potential can rotate in the poloidal direction with the typical velocity of 100m/s, similar in value with the phase velocity of the m =1 magnetic mode; or it can jump between inboard and outboard equatorial midplane. Moreover, when the floating potential structure rotates, there are preliminary indications that its direction depends on the plasma density: it follows the m =1 mode at higher density, and rotates in the opposite direction at lower density.

  16. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    NASA Astrophysics Data System (ADS)

    Vogt, Dominik Walter; Leonhardt, Rainer

    2016-07-01

    We demonstrate broadband, low loss, and close-to-zero dispersion guidance of terahertz (THz) radiation in a dielectric tube with an anti-reflection structure (AR-tube waveguide) in the frequency range from 0.2 to 1.0 THz. The anti-reflection structure (ARS) consists of close-packed cones in a hexagonal lattice arranged on the outer surface of the tube cladding. The feature size of the ARS is in the order of the wavelength between 0.2 and 1.0 THz. The waveguides are fabricated with the versatile and cost efficient 3D-printing method. Terahertz time-domain spectroscopy (THz-TDS) measurements as well as 3D finite-difference time-domain simulations (FDTD) are performed to extensively characterize the AR-tube waveguides. Spectrograms, attenuation spectra, effective phase refractive indices, and the group-velocity dispersion parameters β 2 of the AR-tube waveguides are presented. Both the experimental and numerical results confirm the extended bandwidth and smaller group-velocity dispersion of the AR-tube waveguide compared to a low loss plain dielectric tube THz waveguide. The AR-tube waveguide prototypes show an attenuation spectrum close to the theoretical limit given by the infinite cladding tube waveguide.

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

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

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

  18. Analysis of simple 2-D and 3-D metal structures subjected to fragment impact

    NASA Technical Reports Server (NTRS)

    Witmer, E. A.; Stagliano, T. R.; Spilker, R. L.; Rodal, J. J. A.

    1977-01-01

    Theoretical methods were developed for predicting the large-deflection elastic-plastic transient structural responses of metal containment or deflector (C/D) structures to cope with rotor burst fragment impact attack. For two-dimensional C/D structures both, finite element and finite difference analysis methods were employed to analyze structural response produced by either prescribed transient loads or fragment impact. For the latter category, two time-wise step-by-step analysis procedures were devised to predict the structural responses resulting from a succession of fragment impacts: the collision force method (CFM) which utilizes an approximate prediction of the force applied to the attacked structure during fragment impact, and the collision imparted velocity method (CIVM) in which the impact-induced velocity increment acquired by a region of the impacted structure near the impact point is computed. The merits and limitations of these approaches are discussed. For the analysis of 3-d responses of C/D structures, only the CIVM approach was investigated.

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

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

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

  20. 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

  1. The effect of sliding velocity on chondrocytes activity in 3D scaffolds.

    PubMed

    Wimmer, Markus A; Alini, Mauro; Grad, Sibylle

    2009-03-11

    Sliding motion and shear are important mediators for the synthesis of cartilage matrix and surface molecules. This study investigated the effects of velocity magnitude and motion path on the response of bovine chondrocytes cultured in polyurethane scaffolds and subjected to oscillation against a ceramic ball. In order to vary velocity magnitude, the ball oscillated +/-25 degrees at 0.01, 0.1, and 1Hz to generate 0.28, 2.8, and 28mm/s, respectively. The median velocity of these 'open' motion trajectories was tested against 'closed' motion trajectories in that the scaffold oscillated +/-20 degrees against the ball at 1Hz, reaching 2.8mm/s. Constructs were loaded twice a day for 1h over 5 days. Gene expression of cartilage oligomeric matrix protein (COMP), proteoglycan 4 (PRG4, lubricin), and hyaluronan synthase 1 (HAS1) and release of COMP, PRG4, and hyaluronan (HA) were analyzed. Velocity magnitude determined both gene expression and release of target molecules. Using regression analysis, there was a positive and significant relationship with all outcome variables. However, only COMP reacted significantly at 0.28mm/s, while all other measured variables were considerably up-regulated at 28mm/s. Motion path characteristics affected COMP, but not PRG4 and HAS1/HA. To conclude, velocity magnitude is a critical determinant for cellular responses in tissue engineered cartilage constructs. The motion type also plays a role. However, different molecules are affected in different ways. A molecule specific velocity threshold appears necessary to induce a significant response. This should be considered in further studies investigating the effects of continuous or intermittent motion. PMID:19152917

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

    PubMed

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

    2008-07-01

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

  3. On the Quality of Velocity Interpolation Schemes for Marker-In-Cell Methods on 3-D Staggered Grids

    NASA Astrophysics Data System (ADS)

    Kaus, B.; Pusok, A. E.; Popov, A.

    2015-12-01

    The marker-in-cell method is generally considered to be a flexible and robust method to model advection of heterogenous non-diffusive properties (i.e. rock type or composition) in geodynamic problems or incompressible Stokes problems. In this method, Lagrangian points carrying compositional information are advected with the ambient velocity field on an immobile, Eulerian grid. However, velocity interpolation from grid points to marker locations is often performed without preserving the zero divergence of the velocity field at the interpolated locations (i.e. non-conservative). Such interpolation schemes can induce non-physical clustering of markers when strong velocity gradients are present (Jenny et al., 2001) and this may, eventually, result in empty grid cells, a serious numerical violation of the marker-in-cell method. Solutions to this problem include: using larger mesh resolutions and/or marker densities, or repeatedly controlling the marker distribution (i.e. inject/delete), but which does not have an established physical background. To remedy this at low computational costs, Jenny et al. (2001) and Meyer and Jenny (2004) proposed a simple, conservative velocity interpolation (CVI) scheme for 2-D staggered grid, while Wang et al. (2015) extended the formulation to 3-D finite element methods. Here, we follow up with these studies and report on the quality of velocity interpolation methods for 2-D and 3-D staggered grids. We adapt the formulations from both Jenny et al. (2001) and Wang et al. (2015) for use on 3-D staggered grids, where the velocity components have different node locations as compared to finite element, where they share the same node location. We test the different interpolation schemes (CVI and non-CVI) in combination with different advection schemes (Euler, RK2 and RK4) and with/out marker control on Stokes problems with strong velocity gradients, which are discretized using a finite difference method. We show that a conservative formulation

  4. A 3-D shear velocity model of the southern North America and the Caribbean plates from ambient noise and earthquake tomography

    NASA Astrophysics Data System (ADS)

    Gaite, B.; Villaseñor, A.; Iglesias, A.; Herraiz, M.; Jiménez-Munt, I.

    2014-10-01

    We use group velocities from earthquake tomography together with group and phase velocities from ambient noise tomography (ANT) of Rayleigh-waves to invert for the 3-D shear-wave velocity structure (5-70 km) of the Caribbean (CAR) and southern North American (NAM) plates. The lithospheric model proposed offers a complete image of the crust and uppermost-mantle with imprints of the tectonic evolution. One of the most striking features inferred is the main role of the Ouachita-Marathon-Sonora orogeny front on the crustal seismic structure of NAM plate. A new imaged feature is the low crustal velocities along USA-Mexico border. The model also shows a break of the E-W mantle velocity dichotomy of the NAM and CAR plates beneath the Isthmus of Tehuantepec and Yucatan Block. High upper-mantle velocities along the Mesoamerican Subduction Zone coincide with inactive volcanic areas while the lowest velocities correspond to active volcanic arcs and thin lithospheric mantle regions.

  5. Earthquake relocation using a 3D a-priori geological velocity model from the western Alps to Corsica: Implication for seismic hazard

    NASA Astrophysics Data System (ADS)

    Béthoux, Nicole; Theunissen, Thomas; Beslier, Marie-Odile; Font, Yvonne; Thouvenot, François; Dessa, Jean-Xavier; Simon, Soazig; Courrioux, Gabriel; Guillen, Antonio

    2016-02-01

    The region between the inner zones of the Alps and Corsica juxtaposes an overthickened crust to an oceanic domain, which makes difficult to ascertain the focal depth of seismic events using routine location codes and average 1D velocity models. The aim of this article is to show that, even with a rather lose monitoring network, accurate routine locations can be achieved by using realistic 3D modelling and advanced location techniques. Previous earthquake tomography studies cover the whole region with spatial resolutions of several tens of kilometres on land, but they fail to resolve the marine domain due to the absence of station coverage and sparse seismicity. To overcome these limitations, we first construct a 3D a-priori P and S velocity model integrating known geophysical and geological information. Significant progress has been achieved in the 3D numerical modelling of complex geological structures by the development of dedicated softwares (e.g. 3D GeoModeller), capable at once of elaborating a 3D structural model from geological and geophysical constraints and, possibly, of refining it by inversion processes (Calcagno et al., 2008). Then, we build an arrival-time catalogue of 1500 events recorded from 2000 to 2011. Hypocentres are then located in this model using a numerical code based on the maximum intersection method (Font et al., 2004), updated by Theunissen et al. (2012), as well as another 3D location technique, the NonLinLoc software (Lomax and Curtis, 2001). The reduction of arrival-time residuals and uncertainties (dh, dz) with respect to classical 1D locations demonstrates the improved accuracy allowed by our approach and confirms the coherence of the 3D geological model built and used in this study. Our results are also compared with previous works that benefitted from the installation of dense temporary networks surrounding the studied epicentre area. The resulting 3D location catalogue allows us to improve the regional seismic hazard assessment

  6. Development of a State-Wide 3-D Seismic Tomography Velocity Model for California

    NASA Astrophysics Data System (ADS)

    Thurber, C. H.; Lin, G.; Zhang, H.; Hauksson, E.; Shearer, P.; Waldhauser, F.; Hardebeck, J.; Brocher, T.

    2007-12-01

    We report on progress towards the development of a state-wide tomographic model of the P-wave velocity for the crust and uppermost mantle of California. The dataset combines first arrival times from earthquakes and quarry blasts recorded on regional network stations and travel times of first arrivals from explosions and airguns recorded on profile receivers and network stations. The principal active-source datasets are Geysers-San Pablo Bay, Imperial Valley, Livermore, W. Mojave, Gilroy-Coyote Lake, Shasta region, Great Valley, Morro Bay, Mono Craters-Long Valley, PACE, S. Sierras, LARSE 1 and 2, Loma Prieta, BASIX, San Francisco Peninsula and Parkfield. Our beta-version model is coarse (uniform 30 km horizontal and variable vertical gridding) but is able to image the principal features in previous separate regional models for northern and southern California, such as the high-velocity subducting Gorda Plate, upper to middle crustal velocity highs beneath the Sierra Nevada and much of the Coast Ranges, the deep low-velocity basins of the Great Valley, Ventura, and Los Angeles, and a high- velocity body in the lower crust underlying the Great Valley. The new state-wide model has improved areal coverage compared to the previous models, and extends to greater depth due to the data at large epicentral distances. We plan a series of steps to improve the model. We are enlarging and calibrating the active-source dataset as we obtain additional picks from investigators and perform quality control analyses on the existing and new picks. We will also be adding data from more quarry blasts, mainly in northern California, following an identification and calibration procedure similar to Lin et al. (2006). Composite event construction (Lin et al., in press) will be carried out for northern California for use in conventional tomography. A major contribution of the state-wide model is the identification of earthquakes yielding arrival times at both the Northern California Seismic

  7. Investigating particle phase velocity in a 3D spouted bed by a novel fiber high speed photography method

    NASA Astrophysics Data System (ADS)

    Qian, Long; Lu, Yong; Zhong, Wenqi; Chen, Xi; Ren, Bing; Jin, Baosheng

    2013-07-01

    A novel fiber high speed photography method has been developed to measure particle phase velocity in a dense gas-solid flow. The measurement system mainly includes a fiber-optic endoscope, a high speed video camera, a metal halide light source and a powerful computer with large memory. The endoscope which could be inserted into the reactors is used to form motion images of particles within the measurement window illuminated by the metal halide lamp. These images are captured by the high speed video camera and processed through a series of digital image processing algorithms, such as calibration, denoising, enhancement and binarization in order to improve the image quality. Then particles' instantaneous velocity is figured out by tracking each particle in consecutive frames. Particle phase velocity is statistically calculated according to the probability of particle velocity in each frame within a time period. This system has been applied to the investigation of particles fluidization characteristics in a 3D spouted bed. The experimental results indicate that the particle fluidization feature in the region investigated could be roughly classified into three sections by particle phase vertical velocity and the boundary between the first section and the second is the surface where particle phase velocity tends to be 0, which is in good agreement with the results published in other literature.

  8. 3D Reconstruction of virtual colon structures from colonoscopy images.

    PubMed

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

    2014-01-01

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

  9. The mantle wedge's transient 3-D flow regime and thermal structure

    NASA Astrophysics Data System (ADS)

    Davies, D. R.; Le Voci, G.; Goes, S.; Kramer, S. C.; Wilson, C. R.

    2016-01-01

    Arc volcanism, volatile cycling, mineralization, and continental crust formation are likely regulated by the mantle wedge's flow regime and thermal structure. Wedge flow is often assumed to follow a regular corner-flow pattern. However, studies that incorporate a hydrated rheology and thermal buoyancy predict internal small-scale-convection (SSC). Here, we systematically explore mantle-wedge dynamics in 3-D simulations. We find that longitudinal "Richter-rolls" of SSC (with trench-perpendicular axes) commonly occur if wedge hydration reduces viscosities to Pa s, although transient transverse rolls (with trench-parallel axes) can dominate at viscosities of Pa s. Rolls below the arc and back arc differ. Subarc rolls have similar trench-parallel and trench-perpendicular dimensions of 100-150 km and evolve on a 1-5 Myr time-scale. Subback-arc instabilities, on the other hand, coalesce into elongated sheets, usually with a preferential trench-perpendicular alignment, display a wavelength of 150-400 km and vary on a 5-10 Myr time scale. The modulating influence of subback-arc ridges on the subarc system increases with stronger wedge hydration, higher subduction velocity, and thicker upper plates. We find that trench-parallel averages of wedge velocities and temperature are consistent with those predicted in 2-D models. However, lithospheric thinning through SSC is somewhat enhanced in 3-D, thus expanding hydrous melting regions and shifting dehydration boundaries. Subarc Richter-rolls generate time-dependent trench-parallel temperature variations of up to K, which exceed the transient 50-100 K variations predicted in 2-D and may contribute to arc-volcano spacing and the variable seismic velocity structures imaged beneath some arcs.

  10. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

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

    2016-05-01

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

  11. Anomalously low amplitude of S waves produced by the 3D structures in the lower mantle

    NASA Astrophysics Data System (ADS)

    To, Akiko; Capdeville, Yann; Romanowicz, Barbara

    2016-07-01

    Direct S and Sdiff phases with anomalously low amplitudes are recorded for the earthquakes in Papua New Guinea by seismographs in northern America. According to the prediction by a standard 1D model, the amplitudes are the lowest at stations in southern California, at a distance and azimuth of around 95° and 55°, respectively, from the earthquake. The amplitude anomaly is more prominent at frequencies higher than 0.03 Hz. We checked and ruled out the possibility of the anomalies appearing because of the errors in the focal mechanism used in the reference synthetic waveform calculations. The observed anomaly distribution changes drastically with a relatively small shift in the location of the earthquake. The observations indicate that the amplitude reduction is likely due to the 3D shear velocity (Vs) structure, which deflects the wave energy away from the original ray paths. Moreover, some previous studies suggested that some of the S and Sdiff phases in our dataset are followed by a prominent postcursor and show a large travel time delay, which was explained by placing a large ultra-low velocity zone (ULVZ) located on the core-mantle boundary southwest of Hawaii. In this study, we evaluated the extent of amplitude anomalies that can be explained by the lower mantle structures in the existing models, including the previously proposed ULVZ. In addition, we modified and tested some models and searched for the possible causes of low amplitudes. Full 3D synthetic waveforms were calculated and compared with the observations. Our results show that while the existing models explain the trends of the observed amplitude anomalies, the size of such anomalies remain under-predicted especially at large distances. Adding a low velocity zone, which is spatially larger and has less Vs reduction than ULVZ, on the southwest side of ULVZ, contributes to explain the low amplitudes observed at distances larger than 100° from the earthquake. The newly proposed low velocity zone

  12. Horizontal Velocity Structure in Waterspouts.

    NASA Astrophysics Data System (ADS)

    Schwiesow, R. L.

    1981-04-01

    We have measured the spatial variation of a single horizontal component of the velocity in a number of waterspouts using an airborne infrared Doppler lidar. In 21 data sets, maximum velocities range from 4.2 to 33.6 m s1 and visible funnel diameters from 6.6 to 90 m. Data were taken at altitudes between 675 m, near cloud base, and 95 m above the surface. The sequences show time development of the velocity as a function of radius at a fixed altitude and the velocity structure at different altitudes and sequential times with a horizontal resolution of 0.75 m between data points. The variation in velocity structure between waterspouts is large, with some showing marked azimuthal asymmetry and mixing with the ambient flow, and others showing multiple concentric vortex shells.

  13. Lapse-time dependent coda-wave depth sensitivity to local velocity perturbations in 3-D heterogeneous elastic media

    NASA Astrophysics Data System (ADS)

    Obermann, Anne; Planès, Thomas; Hadziioannou, Céline; Campillo, Michel

    2016-07-01

    In the context of seismic monitoring, recent studies made successful use of seismic coda waves to locate medium changes on the horizontal plane. Locating the depth of the changes, however, remains a challenge. In this paper, we use 3-D wavefield simulations to address two problems: firstly, we evaluate the contribution of surface and body wave sensitivity to a change at depth. We introduce a thin layer with a perturbed velocity at different depths and measure the apparent relative velocity changes due to this layer at different times in the coda and for different degrees of heterogeneity of the model. We show that the depth sensitivity can be modelled as a linear combination of body- and surface-wave sensitivity. The lapse-time dependent sensitivity ratio of body waves and surface waves can be used to build 3-D sensitivity kernels for imaging purposes. Secondly, we compare the lapse-time behavior in the presence of a perturbation in horizontal and vertical slabs to address, for instance, the origin of the velocity changes detected after large earthquakes.

  14. Triangular framework mesh generation of 3D geological structure

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  15. 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.

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

    PubMed

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

    2016-04-01

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

  17. On the location of microseismic sources in instable rock slope areas: heterogeneous vs. homogenous 3D velocity models

    NASA Astrophysics Data System (ADS)

    Coviello, Velio; Manconi, Andrea; Occhiena, Cristina; Arattano, Massimo; Scavia, Claudio

    2013-04-01

    Rock-falls are one of the most common and hazardous phenomena occurring in mountainous areas. The formation of cracks in rocks is often accompanied by a sudden release of energy, which propagates in form of elastic waves and can be detected by a suitable transducer array. Therefore, geophones are among the most effective monitoring devices to investigate eventual precursors of rock-fall phenomena. However, the identification of an efficient procedure to forecast rock-fall occurrence in space and time is still an open challenge. In this study, we aim at developing an efficient procedure to locate microseismic sources relevant to cracking mechanisms, and thus gather indications on eventual precursors of rock-fall phenomena. Common seismic location tools usually implement homogeneous or multilayered velocity models but, in case of high slope gradients and heavily fractured rock masses, these simplifications may lead to errors on the correct estimation of the source location. Thus, we analyzed how the consideration of 3D material properties on the propagation medium may influence the location. In the framework of the Alcotra 2007-2013 Project MASSA (Medium And Small Size rock-fall hazard Assessment), a monitoring system composed by 8 triaxial geophones was installed in 2010 at the J.A. Carrel hut (3829 m a.s.l., Matterhorn, NW Italian Alps) and during the first year of operation the network recorded more than 600 natural events that exceeded a fixed threshold [1]. Despite the harsh environmental conditions of the study area, eighteen points distributed as uniformly as possible in space were selected for hammering. The artificial source dataset of known coordinates was used to constrain a 3D heterogeneous velocity model through a Simultaneous Iterative Reconstructive Technique. In order to mitigate the intrinsic uncertainties of the inversion procedure, bootstrapping was performed to extend the dataset and a statistical analysis was issued to improve the model

  18. 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

  19. Present-Day 3D Velocity Field of Eastern North America Based on Continuous GPS Observations

    NASA Astrophysics Data System (ADS)

    Goudarzi, Mohammad Ali; Cocard, Marc; Santerre, Rock

    2016-07-01

    The Saint Lawrence River valley in eastern Canada was studied using observations of continuously operating GPS (CGPS) stations. The area is one of the most seismically active regions in eastern North America characterized by many earthquakes, which is also subject to an ongoing glacial isostatic adjustment. We present the current three-dimensional velocity field of eastern North America obtained from more than 14 years (9 years on average) of data at 112 CGPS stations. Bernese GNSS and GITSA software were used for CGPS data processing and position time series analysis, respectively. The results show the counterclockwise rotation of the North American plate in the No-Net-Rotation model with the average of 16.8 ± 0.7 mm/year constrained to ITRF 2008. We also present an ongoing uplift model for the study region based on the present-day CGPS observations. The model shows uplift all over eastern Canada with the maximum rate of 13.7 ± 1.2 mm/year and subsidence to the south mainly over northern USA with a typical rate of -1 to -2 mm/year and the minimum value of -2.7 ± 1.4 mm/year. We compared our model with the rate of radial displacements from the ICE-5G model. Both models agree within 0.02 mm/year at the best stations; however, our model shows a systematic spatial tilt compared to ICE-5G. The misfits between two models amount to the maximum relative subsidence of -6.1 ± 1.1 mm/year to the east and maximum relative uplift of 5.9 ± 2.7 mm/year to the west. The intraplate horizontal velocities are radially outward from the centers of maximum uplift and are inward to the centers of maximum subsidence with the typical velocity of 1-1.6 ± 0.4 mm/year that is in agreement with the ICE-5G model to the first order.

  20. Present-Day 3D Velocity Field of Eastern North America Based on Continuous GPS Observations

    NASA Astrophysics Data System (ADS)

    Goudarzi, Mohammad Ali; Cocard, Marc; Santerre, Rock

    2016-03-01

    The Saint Lawrence River valley in eastern Canada was studied using observations of continuously operating GPS (CGPS) stations. The area is one of the most seismically active regions in eastern North America characterized by many earthquakes, which is also subject to an ongoing glacial isostatic adjustment. We present the current three-dimensional velocity field of eastern North America obtained from more than 14 years (9 years on average) of data at 112 CGPS stations. Bernese GNSS and GITSA software were used for CGPS data processing and position time series analysis, respectively. The results show the counterclockwise rotation of the North American plate in the No-Net-Rotation model with the average of 16.8 ± 0.7 mm/year constrained to ITRF 2008. We also present an ongoing uplift model for the study region based on the present-day CGPS observations. The model shows uplift all over eastern Canada with the maximum rate of 13.7 ± 1.2 mm/year and subsidence to the south mainly over northern USA with a typical rate of -1 to -2 mm/year and the minimum value of -2.7 ± 1.4 mm/year. We compared our model with the rate of radial displacements from the ICE-5G model. Both models agree within 0.02 mm/year at the best stations; however, our model shows a systematic spatial tilt compared to ICE-5G. The misfits between two models amount to the maximum relative subsidence of -6.1 ± 1.1 mm/year to the east and maximum relative uplift of 5.9 ± 2.7 mm/year to the west. The intraplate horizontal velocities are radially outward from the centers of maximum uplift and are inward to the centers of maximum subsidence with the typical velocity of 1-1.6 ± 0.4 mm/year that is in agreement with the ICE-5G model to the first order.

  1. A Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location

    NASA Astrophysics Data System (ADS)

    Ballard, S.; Young, C. J.; Hipp, J. R.; Chang, M.; Lewis, J.; Begnaud, M. L.; Rowe, C. A.

    2009-12-01

    further refinement takes place around adjusted nodes to form a new model, and the process is repeated until no more improvement can be obtained. We thus produce a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. This scheme is computationally expensive, so we use a Java-based distributed computing framework developed by Sandia National Laboratories (SNL), providing us with 300+ processors having an efficiency of better than 90% for the calculations. We evaluate our model both in terms of travel time residual variance reduction and in location improvement for GT events. For the latter, we use a new multi-threaded version of the SNL-developed LocOO code modified to use 3D velocity models.

  2. A Robust Method to Detect Zero Velocity for Improved 3D Personal Navigation Using Inertial Sensors

    PubMed Central

    Xu, Zhengyi; Wei, Jianming; Zhang, Bo; Yang, Weijun

    2015-01-01

    This paper proposes a robust zero velocity (ZV) detector algorithm to accurately calculate stationary periods in a gait cycle. The proposed algorithm adopts an effective gait cycle segmentation method and introduces a Bayesian network (BN) model based on the measurements of inertial sensors and kinesiology knowledge to infer the ZV period. During the detected ZV period, an Extended Kalman Filter (EKF) is used to estimate the error states and calibrate the position error. The experiments reveal that the removal rate of ZV false detections by the proposed method increases 80% compared with traditional method at high walking speed. Furthermore, based on the detected ZV, the Personal Inertial Navigation System (PINS) algorithm aided by EKF performs better, especially in the altitude aspect. PMID:25831086

  3. A robust method to detect zero velocity for improved 3D personal navigation using inertial sensors.

    PubMed

    Xu, Zhengyi; Wei, Jianming; Zhang, Bo; Yang, Weijun

    2015-01-01

    This paper proposes a robust zero velocity (ZV) detector algorithm to accurately calculate stationary periods in a gait cycle. The proposed algorithm adopts an effective gait cycle segmentation method and introduces a Bayesian network (BN) model based on the measurements of inertial sensors and kinesiology knowledge to infer the ZV period. During the detected ZV period, an Extended Kalman Filter (EKF) is used to estimate the error states and calibrate the position error. The experiments reveal that the removal rate of ZV false detections by the proposed method increases 80% compared with traditional method at high walking speed. Furthermore, based on the detected ZV, the Personal Inertial Navigation System (PINS) algorithm aided by EKF performs better, especially in the altitude aspect. PMID:25831086

  4. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

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

    2016-05-01

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

  5. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2009-01-01

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

  7. On the 3D structure of the nebula around η-Carinae

    NASA Astrophysics Data System (ADS)

    Zaninetti, L.

    2010-12-01

    The asymmetric shape of the nebula around η-Carinae (Homunculus) can be explained by a spherical expansion in a non-homogeneous medium. Two models are analyzed: an exponential and an inverse power law dependence for the density as a function of distance from the equatorial plane. The presence of a medium with variable density along the polar direction progressively converts the original spherical shell into a bipolar nebula. In the case of the nebula around η-Carinae, we know the time elapsed since the great outburst in 1840. An exact match between observed radii and velocities can be obtained by fine tuning the parameters involved, such as initial radius, initial velocity and the typical scale that characterizes the gradient in density. The observed radius and velocity of the Homunculus as a function of the polar angle in spherical coordinates can be compared with the corresponding simulated data by introducing the efficiency in a single or multiple directions. Once the 3D spatial structure of the Homunculus is obtained, we can compose the image by integrating along the line of sight. In order to simulate the observed image, we have considered a bipolar nebula with constant thickness and an optically thin emitting layer. Some simulated cuts of the relative intensity are reported and may represent a useful reference for the astronomical cuts.

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

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

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

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

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-07-01

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

  12. 3D structural model of the North Alpine Foreland Basin, Bavarian Part

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  13. 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…

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

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

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

  15. 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.

  16. Global Structure of Idealized Stream Interaction Regions Using 3D MHD Simulations

    NASA Astrophysics Data System (ADS)

    Pahud, D. M.; Hughes, W. J.; Merkin, V. G.

    2014-12-01

    The global structure of the heliosphere during solar cycles (SC) 23 and 24 differed significantly in many ways, for example in terms of global magnetic field strength, velocity structure and the observed properties of Stream Interaction Region (SIR) and associated shocks. The differences considered in this study focus primarily on the effects of the three-dimensional (3D) structure of SIRs. During the minimum of SC 24, equatorial coronal holes were prevalent as sources of low-latitude high-speed solar wind. In contrast, the canonical depiction of SC 23's minimum wind configuration is of a band of slow wind undulating about the heliographic equator. Using the heliospheric adaptation of the Lyon-Fedder-Mobarry magnetohydrodynamic (MHD) model (LFM-helio), we have run simulations for two idealized global solar wind conditions. The first simulation approximates the classical tilted dipole, with fast solar wind at high latitudes and a band of slow wind tilted with respect to the heliographic equator, and the second consists of global slow solar wind with equatorial circular sources of high-speed streams. The evolution of the SIRs from 0.1 AU to 2.0 AU is characterized using the amplitude and location of the maximum compressions of the plasma and the magnetic field as well as the largest deflection of solar wind flow. The relation between plasma and magnetic field compressions differs between the two cases considered. The SIRs produced by the equatorial coronal holes have similar maximum densities to those of the tilted dipole case, but the magnetic field magnitude is larger and the plasma is hotter. This suggests that evolution depends on the 3D structure of the SIR and its effects on the competitive roles of the growth of the structure, driven by compression from dynamic pressure, and and relaxation from the plasma flow and magnetic field deflections occurring in the region. Magnetic field threading SIRs and tracing plasma parcels are examined.

  17. 3D Thermoelectric Structures Derived from a New Mixed Micromachining Process

    NASA Astrophysics Data System (ADS)

    Du, Chen-Hsun; Lee, Chengkuo

    2000-12-01

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

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

    PubMed

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

    2007-01-01

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

  19. Delineation of nuclear structures in 3D multicellular systems

    2013-09-13

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

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

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

  2. 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

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

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2016-08-01

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

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

    1999-11-22

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

  7. 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.

  8. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

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

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

  9. 3D tomographic reconstruction of the internal velocity field of an immiscible drop in a shear flow

    NASA Astrophysics Data System (ADS)

    Kerdraon, Paul; Dalziel, Stuart B.; Goldstein, Raymond E.; Landel, Julien R.; Peaudecerf, Francois J.

    2015-11-01

    We study experimentally the internal flow of a drop attached to a flat substrate and immersed in an immiscible shear flow. Transport inside the drop can play a crucial role in cleaning applications. Internal advection can enhance the mass transfer across the drop surface, thus increasing the cleaning rate. We used microlitre water-glycerol drops on a hydrophobic substrate. The drops were spherical and did not deform significantly under the shear flow. An oil phase of relative viscosity 0.01 to 1 was flowed over the drop. Typical Reynolds numbers inside the drops were of the order of 0.1 to 10. Using confocal microscopy, we performed 3D tomographic reconstruction of the flow field in the drop. The in-plane velocity field was measured using micro-PIV, and the third velocity component was computed from incompressibility. To our knowledge, this study gives the first experimental measurement of the three-dimensional internal velocity field of a drop in a shear flow. Numerical simulations and theoretical models published in the past 30 years predict a toroidal internal recirculation flow, for which the entire surface flows streamwise. However, our measurements reveal a qualitatively different picture with a two-lobed recirculation, featuring two stagnation points at the surface and a reverse surface flow closer to the substrate. This finding appears to be independent of Reynolds number and viscosity ratio in the ranges studied; we conjecture that the observed flow is due to the effect of surfactants at the drop surface.

  10. The 3-D strain patterns in Turkey using geodetic velocity fields from the RTK-CORS (TR) network

    NASA Astrophysics Data System (ADS)

    Kutoglu, Hakan Senol; Toker, Mustafa; Mekik, Cetin

    2016-03-01

    This study presents our use of GPS data to obtain and quantify the full continuous strain tensor using a 3-D velocity field in Turkey. In this study, GPS velocities improve the estimation of short-term strain tensor fields for determining the seismic hazard of Turkey. The tensorial analysis presents different aspects of deformation, such as the normal and shear strains, including their directions, the compressional and extensional strains. This analysis is appropriate for the characterizing the state of the current seismic deformation. GPS velocity data from continuous measurements (2009-2012) to estimate deformations were processed using the GAMIT/GLOBK software. Using high-rate GPS data from permanent 146 GNSS stations (RTK-CORS-TR network), the strain distribution was determined and interpolated using a biharmonic spline technique. We show the strain field patterns within axial and plane form at several critical locations, and discuss these results within the context of the seismic and tectonic deformation of Turkey. We conclude that the knowledge of the crustal strain patterns provides important information on the location of the main faults and strain accumulation for the hazard assessment. The results show an agreement between the seismic and tectonic strains confirming that there are active crustal deformations in Turkey.

  11. Loads and pressure evaluation of the flow around a flapping wing from instantaneous 3D velocity measurements

    NASA Astrophysics Data System (ADS)

    Tronchin, Thibaut; David, Laurent; Farcy, Alain

    2015-01-01

    The flow around a flapping wing is characterized by an unsteady evolution of three-dimensional vortices, which are one of the main sources of loads. The difficulty in directly measuring such low forces by means of sensors and the need of the characterization of the evolution of the flow have lead to the evaluation of loads using the integral form of the momentum equation. This paper describes methods for evaluating instantaneous loads and three-dimensional pressure fields using 3D3C velocity fields only. An evaluation of the accuracy of these methods using DNS velocity fields is presented. Loads and pressure fields are then calculated using scanning tomography PIV velocity fields, around a NACA 0012 airfoil for a flapping motion in a water tank at a Reynolds number of 1,000. The results suggest a sufficient accuracy of calculated pressure fields for a global analysis of the topology of the flow and for the evaluation of loads by integrating the calculated pressure field over the surface of the wing.

  12. 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.

  13. 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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  16. A compact single-camera system for high-speed, simultaneous 3-D velocity and temperature measurements.

    SciTech Connect

    Lu, Louise; Sick, Volker; Frank, Jonathan H.

    2013-09-01

    The University of Michigan and Sandia National Laboratories collaborated on the initial development of a compact single-camera approach for simultaneously measuring 3-D gasphase velocity and temperature fields at high frame rates. A compact diagnostic tool is desired to enable investigations of flows with limited optical access, such as near-wall flows in an internal combustion engine. These in-cylinder flows play a crucial role in improving engine performance. Thermographic phosphors were proposed as flow and temperature tracers to extend the capabilities of a novel, compact 3D velocimetry diagnostic to include high-speed thermometry. Ratiometric measurements were performed using two spectral bands of laser-induced phosphorescence emission from BaMg2Al10O17:Eu (BAM) phosphors in a heated air flow to determine the optimal optical configuration for accurate temperature measurements. The originally planned multi-year research project ended prematurely after the first year due to the Sandia-sponsored student leaving the research group at the University of Michigan.

  17. 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).

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

    PubMed

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

    2016-03-01

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

  19. 3D Structured Grid Generation Codes for Turbomachinery

    NASA Technical Reports Server (NTRS)

    Loellbach, James; Tsung, Fu-Lin

    1999-01-01

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

  20. 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.

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  4. Hypocenter relocation using a fast grid search method and a 3-D seismic velocity model for the Sumatra region

    SciTech Connect

    Nugroho, Hendro; Widiyantoro, Sri; Nugraha, Andri Dian

    2013-09-09

    Determination of earthquake hypocenter in Indonesia conducted by the Meteorological, Climatological, and Geophysical Agency (MCGA) has still used a 1-D seismic velocity model. In this research, we have applied a Fast Grid Search (FGM) method and a 3-D velocity model resulting from tomographic imaging to relocate earthquakes in the Sumatran region. The data were taken from the MCGA data catalog from 2009 to 2011 comprising of subduction zone and on land fault earthquakes with magnitude greater than 4 Mw. Our preliminary results show some significant changes in the depths of the relocated earthquakes which are in general deeper than the depths of hypocenters from the MCGA data catalog. The residual times resulting from the relocation process are smaller than those prior to the relocation. Encouraged by these results, we will continue to conduct hypocenter relocation for all events from the MCGA data catalog periodically in order to produce a new data catalog with good quality. We hope that the new data catalog will be useful for further studies.

  5. 'Distance mapping' and the 3D structure of BD +30° 3639

    NASA Astrophysics Data System (ADS)

    Akras, S.; Steffen, W.

    2012-06-01

    BD +30° 3639 is a member of a group of uncommon planetary nebulae with Wolf-Rayet central star and higher expansion velocities in [O III] than in [N II] lines. Images and high-resolution spectra from the literature are used in order to construct a 3D model of the nebula using the morpho-kinematic code SHAPE. We find that two homologous expansion laws are needed for the [N II] and [O III] shells. We conclude that the internal velocity field of BD +30° 3639 decreases with the distance from the central star at least between the [O III] and [N II] shells. A cylindrical velocity component is used to replicate the high-speed bipolar collimated outflows. We also present a new kinematic analysis technique called 'distance mapping'. It uses the observed proper motion vectors and the 3D velocity field to generate maps that can be used as a constraint to the morpho-kinematic modelling with SHAPE as well as improve the accuracy for distance determination. It is applied to BD +30° 3639 using 178 internal proper motion vectors from Li, Harrington & Borkowski and our 3D velocity field to determine a distance of 1.52 ± 0.21 kpc. Finally, we find evidence for an interaction between the eastern part of the nebula and the ambient H2 molecular gas.

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

    PubMed

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

    2016-05-01

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

  7. 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.

  8. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  9. 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.

  10. Seismicity and Improved Velocity Structure in Kuwait

    SciTech Connect

    Gok, R M; Rodgers, A J; Al-Enezi, A

    2006-01-26

    The Kuwait National Seismic Network (KNSN) began operation in 1997 and consists of nine three-component stations (eight short-period and one broadband) and is operated by the Kuwait Institute for Scientific Research. Although the region is largely believed to be aseismic, considerable local seismicity is recorded by KNSN. Seismic events in Kuwait are clustered in two main groups, one in the south and another in the north. The KNSN station distribution is able to capture the southern cluster within the footprint of the network but the northern cluster is poorly covered. Events tend to occur at depths ranging from the free surface to about 20 km. Events in the northern cluster tend to be deeper than those in south, however this might be an artifact of the station coverage. We analyzed KNSN recordings of nearly 200 local events to improve understanding of seismic events and crustal structure in Kuwait, performing several analyses with increasing complexity. First, we obtained an optimized one-dimensional (1D) velocity model for the entire region using the reported KNSN arrival times and routine locations. The resulting model is consistent with a recently obtained model from the joint inversion of receiver functions and surface wave group velocities. Crustal structure is capped by the thick ({approx} 7 km) sedimentary rocks of the Arabian Platform underlain by normal velocities for stable continental crust. Our new model has a crustal thickness of 44 km, constrained by an independent study of receiver functions and surface wave group velocities by Pasyanos et al (2006). Locations and depths of events after relocation with the new model are broadly consistent with those reported by KISR, although a few events move more than a few kilometers. We then used a double-difference tomography technique (tomoDD) to jointly locate the events and estimate three-dimensional (3D) velocity structure. TomoDD is based on hypoDD relocation algorithm and it makes use of both absolute and

  11. Test of high-resolution 3D P-wave velocity model of Poland by back-azimuthal sections of teleseismic receiver function

    NASA Astrophysics Data System (ADS)

    Wilde-Piorko, Monika; Polkowski, Marcin; Grad, Marek

    2015-04-01

    Geological and seismic structure under area of Poland is well studied by over one hundred thousand boreholes, over thirty deep seismic refraction and wide angle reflection profiles and by vertical seismic profiling, magnetic, gravity, magnetotelluric and thermal methods. Compilation of these studies allowed to create a high-resolution 3D P-wave velocity model down to 60 km depth in the area of Poland (Polkowski et al. 2014). Model also provides details about the geometry of main layers of sediments (Tertiary and Quaternary, Cretaceous, Jurassic, Triassic, Permian, old Paleozoic), consolidated/crystalline crust (upper, middle and lower) and uppermost mantle. This model gives an unique opportunity for calculation synthetic receiver function and compering it with observed receiver function calculated for permanent and temporary seismic stations. Modified ray-tracing method (Langston, 1977) can be used directly to calculate the response of the structure with dipping interfaces to the incoming plane wave with fixed slowness and back-azimuth. So, 3D P-wave velocity model has been interpolated to 2.5D P-wave velocity model beneath each seismic station and back-azimuthal sections of components of receiver function have been calculated. Vp/Vs ratio is assumed to be 1.8, 1.67, 1.73, 1.77 and 1.8 in the sediments, upper/middle/lower consolidated/crystalline crust and uppermost mantle, respectively. Densities were calculated with combined formulas of Berteussen (1977) and Gardner et al. (1974). Additionally, to test a visibility of the lithosphere-asthenosphere boundary phases at receiver function sections models have been extended to 250 km depth based on P4-mantle model (Wilde-Piórko et al., 2010). National Science Centre Poland provided financial support for this work by NCN grant DEC-2011/02/A/ST10/00284 and by NCN grant UMO-2011/01/B/ST10/06653.

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

    NASA Astrophysics Data System (ADS)

    Rybakov, M.

    2009-12-01

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

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

    PubMed

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

    2012-05-30

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

  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. A high-resolution 3D seismic velocity model of the 2010 Mw 8.8 Maule, Chile earthquake rupture zone using land & OBS networks

    NASA Astrophysics Data System (ADS)

    Hicks, S. P.; Rietbrock, A.; Ryder, I. M.; Miller, M.; Lee, C.

    2013-12-01

    Knowledge of seismic properties along a subduction megathrust can shed light on the composition and structure of rocks along the fault. By comparing seismic velocity structure with models of interseismic locking, co-seismic slip and afterslip, we can begin to understand how physical properties may affect fault dynamics throughout the subduction seismic cycle. The Maule earthquake, which hit the coast of central Chile in 2010, is the 6th largest earthquake ever recorded, rupturing a 500 x 80 km area of the Chilean megathrust. Published models demonstrate a complex bilateral rupture, with most co-seismic slip occurring to the north of the mainshock epicentre, although significant slip likely stopped short of the trench and the continental Moho. Here, we show a new high-resolution 3D velocity model (vp and vp/vs ratio) of the central Chilean margin Our velocity model is based on manually picked P- and S-wave arrival times from 670 aftershocks recorded by the International Maule Aftershock Deployment (IMAD) network. Seismic properties of the marine forearc are poorly understood in subduction zones, but by incorporating picks from two ocean-bottom seismometer (OBS) networks, we can resolve the velocity structure of the megathrust as far as the trench. In total, the catalogue used for the tomographic inversion yields a total of ~50,000 high quality P- and S-wave picks. We analyse the quality of our model by analysis of the resolution matrix and by testing characteristic models. The 3D velocity model shows the main structures associated within a subduction forearc: the marine forearc basin (vp < 6.0 km/s), continental mantle (vp > 7.5 km/s), and subducting oceanic crust (vp ~ 7.7 km/s). The plate interface is well defined by relocated aftershock seismicity. P-wave velocities along the megathrust range from 6.5 km/s beneath the marine forearc to 7.7 km/s at the intersection of the megathrust with the continental Moho. We infer several high vp anomalies within the South

  16. 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.

  17. 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

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

    PubMed

    Zhang, Fengxiang; Low, Hong Yee

    2008-10-15

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

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

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

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

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  3. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  5. Global well-posedness to the 3-D incompressible inhomogeneous Navier-Stokes equations with a class of large velocity

    NASA Astrophysics Data System (ADS)

    Zhai, Cuili; Zhang, Ting

    2015-09-01

    In this article, we consider the global well-posedness to the 3-D incompressible inhomogeneous Navier-Stokes equations with a class of large velocity. More precisely, assuming a 0 ∈ B˙ q , 1 /3 q ( R 3 ) and u 0 = ( u0 h , u0 3 ) ∈ B˙ p , 1 - 1 + /3 p ( R 3 ) for p, q ∈ (1, 6) with sup ( /1 p , /1 q ) ≤ /1 3 + inf ( /1 p , /1 q ) , we prove that if C a↑0↑ B˙q1/3 q α (↑u0 3↑ B˙ p , 1 - 1 + /3 p/μ + 1 ) ≤ 1 , /C μ (↑u0 h↑ B˙ p , 1 - 1 + /3 p + ↑u03↑ B˙ p , 1 - 1 + /3 p 1 - α ↑u0h↑ B˙ p , 1 - 1 + /3 p α) ≤ 1 , then the system has a unique global solution a ∈ C ˜ ( [ 0 , ∞ ) ; B˙ q , 1 /3 q ( R 3 ) ) , u ∈ C ˜ ( [ 0 , ∞ ) ; B˙ p , 1 - 1 + /3 p ( R 3 ) ) ∩ L 1 ( R + ; B˙ p , 1 1 + /3 p ( R 3 ) ) . It improves the recent result of M. Paicu and P. Zhang [J. Funct. Anal. 262, 3556-3584 (2012)], where the exponent form of the initial smallness condition is replaced by a polynomial form.

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

    PubMed

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

    2010-09-27

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  8. Direct measurement of particle size and 3D velocity of a gas-solid pipe flow with digital holographic particle tracking velocimetry.

    PubMed

    Wu, Yingchun; Wu, Xuecheng; Yao, Longchao; Gréhan, Gérard; Cen, Kefa

    2015-03-20

    The 3D measurement of the particles in a gas-solid pipe flow is of great interest, but remains challenging due to curved pipe walls in various engineering applications. Because of the astigmatism induced by the pipe, concentric ellipse fringes in the hologram of spherical particles are observed in the experiments. With a theoretical analysis of the particle holography by an ABCD matrix, the in-focus particle image can be reconstructed by the modified convolution method and fractional Fourier transform. Thereafter, the particle size, 3D position, and velocity are simultaneously measured by digital holographic particle tracking velocimetry (DHPTV). The successful application of DHPTV to the particle size and 3D velocity measurement in a glass pipe's flow can facilitate its 3D diagnostics. PMID:25968543

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  10. S-wave velocity structure of the North China from inversion of Rayleigh wave phase velocity

    NASA Astrophysics Data System (ADS)

    Chen, Hao-peng; Zhu, Liang-bao; Wang, Qing-dong; Zhang, Pan; Yang, Ying-hang

    2014-07-01

    We constructed the S-wave velocity structure of the crust and uppermost mantle (10-100 km) beneath the North China based on the teleseismic data recorded by 187 portable broadband stations deployed in this region. The traditional two-step inversion scheme was adopted. Firstly, we measured the interstation fundamental Rayleigh wave phase velocity of 10-60 s and imaged the phase velocity distributions using the Tarantola inversion method. Secondly, we inverted the 1-D S-wave velocity structure with a grid spacing of 0.25° × 0.25° and constructed the 3-D S-wave velocity structure of the North China. The 3-D S-wave velocity model provides valuable information about the destruction mechanism and geodynamics of the North China Craton (NCC). The S-wave velocity structures in the northwestern and southwestern sides of the North-South Gravity Lineament (NSGL) are obviously different. The southeastern side is high velocity (high-V) while the northeastern side is low velocity (low-V) at the depth of 60-80 km. The upwelling asthenosphere above the stagnated Pacific plate may cause the destruction of the Eastern Block and form the NSGL. A prominent low-V anomaly exists around Datong from 50 to 100 km, which may due to the upwelling asthenosphere originating from the mantle transition zone beneath the Western Block. The upwelling asthenosphere beneath the Datong may also contribute to the destruction of the Eastern Block. The Zhangjiakou-Penglai fault zone (ZPFZ) may cut through the lithosphere and act as a channel of the upwelling asthenosphere. A noticeable low-V zone also exists in the lower crust and upper mantle lid (30-50 km) beneath the Beijing-Tianjin-Tangshan (BTT) region, which may be caused by the upwelling asthenosphere through the ZPFZ.

  11. High-resolution 3-D S-wave Tomography of upper crust structures in Yilan Plain from Ambient Seismic Noise

    NASA Astrophysics Data System (ADS)

    Chen, Kai-Xun; Chen, Po-Fei; Liang, Wen-Tzong; Chen, Li-Wei; Gung, YuanCheng

    2015-04-01

    The Yilan Plain (YP) in NE Taiwan locates on the western YP of the Okinawa Trough and displays high geothermal gradients with abundant hot springs, likely resulting from magmatism associated with the back-arc spreading as attested by the offshore volcanic island (Kueishantao). YP features NS distinctive characteristics that the South YP exhibits thin top sedimentary layer, high on-land seismicity and significant SE movements, relative those of the northern counterpart. A dense network (~2.5 km station interval) of 89 Texan instruments was deployed in Aug. 2014, covering most of the YP and its vicinity. The ray path coverage density of each 0.015 degree cells are greater than 150 km that could provide the robustness assessment of tomographic results. We analyze ambient noise signals to invert a high-resolution 3D S-wave model for shallow velocity structures in and around YP. The aim is to investigate the velocity anomalies corresponding to geothermal resources and the NS geological distinctions aforementioned. We apply the Welch's method to generate empirical Rayleigh wave Green's functions between two stations records of continuous vertical components. The group velocities of thus derived functions are then obtained by the multiple-filter analysis technique measured at the frequency range between 0.25 and 1 Hz. Finally, we implement a wavelet-based multi-scale parameterization technique to construct 3D model of S-wave velocity. Our first month results exhibit low velocity in the plain, corresponding existing sediments, those of whole YP show low velocity offshore YP and those of high-resolution south YP reveal stark velocity contrast across the Sanshin fault. Key words: ambient seismic noises, Welch's method, S-wave, Yilan Plain

  12. 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

  13. Background and pickup ion velocity distribution dynamics in Titan's plasma environment: 3D hybrid simulation and comparison with CAPS T9 observations

    NASA Astrophysics Data System (ADS)

    Lipatov, A. S.; Sittler, E. C.; Hartle, R. E.; Cooper, J. F.; Simpson, D. G.

    2011-09-01

    In this report we discuss the ion velocity distribution dynamics from the 3D hybrid simulation. In our model the background, pickup, and ionospheric ions are considered as a particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. We also take into account the collisions between the ions and neutrals. The current simulation shows that mass loading by pickup ions H,H2+, CH4+ and N2+ is stronger than in the previous simulations when O + ions are introduced into the background plasma. In our hybrid simulations we use Chamberlain profiles for the atmospheric components. We also include a simple ionosphere model with average mass M = 28 amu ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS T9 observations. Our simulation shows an asymmetry of the ion density distribution and the magnetic field, including the formation of the Alfvén wing-like structures. The simulation also shows that the ring-like velocity distribution for pickup ions relaxes to a Maxwellian core and a shell-like halo.

  14. Background and Pickup Ion Velocity Distribution Dynamics in Titan's Plasma Environment: 3D Hybrid Simulation and Comparison with CAPS T9 Observations

    NASA Technical Reports Server (NTRS)

    Lipatov, A. S.; Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Simpson, D. G.

    2011-01-01

    In this report we discuss the ion velocity distribution dynamics from the 3D hybrid simulation. In our model the background, pickup, and ionospheric ions are considered as a particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. We also take into account the collisions between the ions and neutrals. The current simulation shows that mass loading by pickup ions H(+); H2(+), CH4(+) and N2(+) is stronger than in the previous simulations when O+ ions are introduced into the background plasma. In our hybrid simulations we use Chamberlain profiles for the atmospheric components. We also include a simple ionosphere model with average mass M = 28 amu ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS T9 observations. Our simulation shows an asymmetry of the ion density distribution and the magnetic field, including the formation of the Alfve n wing-like structures. The simulation also shows that the ring-like velocity distribution for pickup ions relaxes to a Maxwellian core and a shell-like halo.

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

    NASA Astrophysics Data System (ADS)

    Ge, Zhaoyang; Hu, Hong; Liu, Yanping

    2013-08-01

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

  16. 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

  17. Relocation of the Waldkirch seismic event, December 5, 2004, with regional 1D- and 3D-velocity models in the presence of upper mantle anisotropy

    NASA Astrophysics Data System (ADS)

    Muench, Thomas; Koch, Manfred; Schlittenhard, Jörg

    2010-05-01

    /VS-ratio across the study area are investigated. Finally a thorough statistical analysis of the hypocentral relocation accuracy and its sensitivity to various observational and model errors is carried out by (1) the classical calculation of covariances and confidence ellipses for the hypocenter and (2) Monte Carlo relocations with random perturbations of the observed arrivaltimes as well as of the choice of the initial hypocenter in the relocation process. The correction of the original phase-data leads to a shift of the hypocenter to about 10 to 15 km depth instead of 0 - 5 km for the uncorrected phases.The importance of the phase correction is also supported by the final RMS which is reduced from 2.22 s to 1.00 s for the isotropic case and, even more so, from 2.29 s to 0.75 s for the anisotropic. The reduced traveltime plots indicate also that a common VP /VS-ratio of 1.72 for both the crust and the upper mantle does not fit the crustal Sg-phases well. From subsequent hypocentral relocations with separate VP/VS-ratio for the crust and the upper mantle optimal values of VP /VS = 1.70 former, respective 1.66 for the latter, are obtained. In a subsequent set of relocations of the Waldkirch event the recently established isotropic and anisotropic 3D- crustal and upper mantle seismic velocity models of (Muench, 2009; Muench et al., 2010) are employed. Compared with the previous 1D hypocentral relocations where the optimal depth range found is 14 to 15 km, those of the 3D models lie about one km higher. The slightly lower depth of the 3D-models is most likely a consequence of traveltime effects of the structural velocity inhomogeneities.

  18. 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.

  19. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography

    PubMed Central

    Ishikawa, Takashi

    2013-01-01

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

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

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

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

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

    PubMed

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

    2016-04-28

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

  2. Dynamics of pickup ion velocity distribution function in Titan's plasma environment (TA encounter): 3D hybrid kinetic modeling and comparison with CAPS observations

    NASA Astrophysics Data System (ADS)

    Simpson, D. G.; Lipatov, A. S.; Sittler, E. C.; Hartle, R. E.; Cooper, J. F.

    2013-12-01

    Wave-particle interactions play a very important role in the plasma dynamics near Titan: mass loading, excitation of the low-frequency waves and the formation of the particle velocity distribution function, e.g. ring/shell-like distributions, etc. The kinetic approach is important for estimation of the collision processes e.g. a charge exchange. The particle velocity distribution function also plays a key role for understanding the observed particle fluxes. In this report we discuss the ion velocity distribution function dynamics from 3D hybrid modeling. The modeling is based on recent analysis of the Cassini Plasma Spectrometer (CAPS) ion measurements during the TA flyby. In our model the background ions, all pickup ions, and ionospheric ions are considered as particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. The temperatures of the background electrons and pickup electrons were also included into the generalized Ohm's law. We also take into account the collisions between the ions and neutrals. We use Chamberlain profiles for the exosphere's components and include a simple ionosphere model with M=28 ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Our modeling shows that interaction between background plasma and pickup ions H+, H2+, CH4+ and N2+ has a more complicated structure than was observed in the T9 flyby and modeling due to the large gyroradius of the background O+ ions [1,2,3,4]. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS TA observations. We also compare our kinetic modeling with other hybrid and MHD modeling of Titan's environment. References [1] Sittler, E.C., et al., Energy Deposition Processes in Titan's Upper Atmosphere and Its Induced Magnetosphere. In: Titan from Cassini-Huygens, Brown, R.H., Lebreton J.P., Waite, J.H., Eds

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

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

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

    PubMed

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

    2016-03-01

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

  8. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

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

    2006-02-01

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

  9. 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

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

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

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

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

    PubMed

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

    2012-05-01

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

  12. 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.

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

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

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

  14. 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.

  15. SERAPIS project - 3D imaging of the Campi Flegrei caldera (southern Italy) : high resolution P-wave velocity tomography

    NASA Astrophysics Data System (ADS)

    Judenherc, S.; Zollo, A.; Auger, E.; Boschi, L.; Satriano, C.; Serapis Working Group

    2003-04-01

    In September 2001, the SERAPIS project was carried out as an extended active seismic survey in the gulfs of Naples and Pozzuoli. A dense array of 60 three-component on-land stations and 72 sea bottom seismographs (OBS) have been deployed to record more than 5000 air gun shots at a spacing of about 125~m. As a preliminary analysis, the first P-arrival times of a the small offset data in the central part of the region has been inverted using the codes of H.M. Benz. The linearized iterative inversion of 38000 arrival times provided a >80% variance reduction with a node spacing of 250m. At the first order, our model shows a 2-layer structure : low velocity volcanic sediments (2.5-3.5km/s) lying on an inclined high velocity limestone platform (>6km/s). The caldera itself is very well identified, the rim is characterized by a 500-1000m upward shift of the velocity isolines. The whole dataset is expected to provide a wider image with the same resolution (250m). It includes the detailed shape of the refractor beneath the caldera as well as its irregularities out of the bay which have been observered in the seismic sections.

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    SciTech Connect

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

    2010-11-10

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

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

    DOEpatents

    Zemla, Adam T.

    2011-09-20

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

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

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

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

  1. 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

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

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

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

  3. 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.

  4. 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.

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

    PubMed

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

    2016-07-01

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

  6. Unified system for 3D holographic displacement and velocity measurements in fluid and solid mechanics: design and construction of the recording camera and interrogation assembly

    NASA Astrophysics Data System (ADS)

    Barnhart, Donald H.; Chan, Victor S. S.; Halliwell, Neil A.; Coupland, Jeremy M.

    1999-10-01

    This paper introduces a new approach to 3D displacement and velocity measurements that unifies the disciplines of holographic interferometry and holographic particle image velocimetry (HPIV). Equally applicable to fluid and solid mechanics, the overall system enables quantitative displacement measurements between two holographically recorded events from either particle or surface scattering sites, working with both pulsed and continuous-wave laser systems. The resulting measurements exhibit an accuracy corresponding to interferometric system, but with a dynamic range found with PIV systems. Most importantly, this paper introduces the novel use of an optical fiber to specify the measurement points, remove optical aberrations of windows, and eliminate directional ambiguity. An optical fiber is used to probe the recorded holographic image space at each 3D measurement point in order to extract the 3D displacement vectors. This fiber system also employs a novel optical image shifting method to eliminate the problem of directional ambiguity. In addition, the reported system uses 3D complex optical correlation rather than 2D real digital correlation. It is therefore a simple matter to directly obtain 3D displacement and velocity measurements at precisely known 3D locations in the object space. By correlating both the amplitude and phase information in the holographic image, this system can measure spatial distributions of displacements even when the presence of severe aberrations preclude the detection of sharp images.

  7. 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

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

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

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

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

    PubMed

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

    2015-03-20

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

  10. 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.

  11. 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.

  12. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

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

    2016-08-19

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

  13. 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.

  14. 3D radiative transfer simulations of Eta Carinae's inner colliding winds - II. Ionization structure of helium at periastron

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    Spectral observations of the massive colliding wind binary Eta Carinae show phase-dependent variations, in intensity and velocity, of numerous helium emission and absorption lines throughout the entire 5.54-yr orbit. Approaching periastron, the 3D structure of the wind-wind interaction region (WWIR) gets highly distorted due to the eccentric (e ˜ 0.9) binary orbit. The secondary star (ηB) at these phases is located deep within the primary's dense wind photosphere. The combination of these effects is thought to be the cause of the particularly interesting features observed in the helium lines at periastron. We perform 3D radiative transfer simulations of η Car's interacting winds at periastron. Using the SIMPLEX radiative transfer algorithm, we post-process output from 3D smoothed particle hydrodynamic simulations of the inner 150 au of the η Car system for two different primary star mass-loss rates (dot{M}_{η A}). Using previous results from simulations at apastron as a guide for the initial conditions, we compute 3D helium ionization maps. We find that, for higher dot{M}_{η A}, ηB He0+-ionizing photons are not able to penetrate into the pre-shock primary wind. He+ due to ηB is only present in a thin layer along the leading arm of the WWIR and in a small region close to the stars. Lowering dot{M}_{η A} allows ηB's ionizing photons to reach the expanding unshocked secondary wind on the apastron side of the system, and create a low fraction of He+ in the pre-shock primary wind. With apastron on our side of the system, our results are qualitatively consistent with the observed variations in strength and radial velocity of η Car's helium emission and absorption lines, which helps better constrain the regions where these lines arise.

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

    PubMed

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

    2015-07-01

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

  16. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

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

    2015-01-01

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

  17. 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.

  18. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

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

    2015-05-05

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

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

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong

    2013-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  3. 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…

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

    PubMed

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

    2013-12-01

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

  5. A high resolution 3D velocity model beneath the Tokyo Metropolitan area by MeSO-net

    NASA Astrophysics Data System (ADS)

    Nakagawa, S.; Sakai, S.; Honda, R.; Kimura, H.; Hirata, N.

    2015-12-01

    Beneath the Tokyo metropolitan area, the Philippine Sea Plate (PSP) subducts and causes devastating mega-thrust earthquakes, such as the 1703 Genroku earthquake (M8.0) and the 1923 Kanto earthquake (M7.9). An M7 or greater (M7+) earthquake in this area at present has high potential to produce devastating serious loss of life and property with even greater global economic repercussions. The Central Disaster Management Council of Japan estimates that an M7+ earthquake will cause 23,000 fatalities and 95 trillion yen (about 1 trillion US$) economic loss. We have launched the Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters in collaboration with scientists, engineers, and social-scientists in nationwide institutions since 2012. We analyze data from the dense seismic array called Metropolitan Seismic Observation network (MeSO-net), which has 296 seismic stations with spacing of 5 km (Sakai and Hirata, 2009; Kasahara et al., 2009). We applied the double-difference tomography method (Zhang and Thurber, 2003) and estimated the velocity structure and the upper boundary of PSP (Nakagawa et al., 2010). The 2011 Tohoku-oki earthquake (M9.0) has activated seismicity also in Kanto region, providing better coverage of ray paths for tomographic analysis. We obtain much higher resolution velocity models from whole dataset observed by MeSO-net between 2008 and 2015. A detailed image of tomograms shows that PSP contacts Pacific plate at a depth of 50 km beneath northern Tokyo bay. A variation of velocity along the oceanic crust suggests dehydration reaction to produce seismicity in a slab, which may related to the M7+ earthquake. Acknowledgement: This study was supported by the Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters of MEXT, Japan and the Earthquake Research Institute cooperative research program.

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Avakian, Harut

    2016-08-01

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

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  12. 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

  13. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  14. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  15. 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

  16. 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.

  17. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    NASA Astrophysics Data System (ADS)

    Zenou, M.; Sa'Ar, A.; Kotler, Z.

    2015-11-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  18. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  19. Ground and Structure Deformation 3d Modelling with a Tin Based Property Model

    NASA Astrophysics Data System (ADS)

    TIAN, T.; Zhang, J.; Jiang, W.

    2013-12-01

    With the development of 3D( three-dimensional) modeling and visualization, more and more 3D tectonics are used to assist the daily work in Engineering Survey, in which the prediction of deformation field in strata and structure induced by underground construction is an essential part. In this research we developed a TIN (Triangulated Irregular Network) based property model for the 3D (three dimensional) visualization of ground deformation filed. By record deformation vector for each nodes, the new model can express the deformation with geometric-deformation-style by drawing each node in its new position and deformation-attribute-distribution-style by drawing each node in the color correspond with its deformation attribute at the same time. Comparing with the volume model based property model, this new property model can provide a more precise geometrical shape for structure objects. Furthermore, by recording only the deformation data of the user-interested 3d surface- such as the ground surface or the underground digging surface, the new property model can save a lot of space, which makes it possible to build the deformation filed model of a much more large scale. To construct the models of deformation filed based on TIN model, the refinement of the network is needed to increase the nodes number, which is necessary to express the deformation filed with a certain resolution. The TIN model refinement is a process of sampling the 3D deformation field values on points on the TIN surface, for which we developed a self-adapting TIN refinement method. By set the parameter of the attribute resolution, this self-adapting method refines the input geometric-expressing TIN model by adding more vertexes and triangles where the 3D deformation filed changing faster. Comparing with the even refinement method, the self-adapting method can generate a refined TIN model with nodes counted less by two thirds. Efficiency Comparison between Self-adapting Refinement Method and Even

  20. Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Wang, Yuan-Fang

    2010-02-01

    We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.

  1. EK3D: an E. coli K antigen 3-dimensional structure database

    PubMed Central

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host–pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  2. Fabrication of 3D microfluidic structures inside glass by femtosecond laser micromachining

    NASA Astrophysics Data System (ADS)

    Sugioka, Koji; Cheng, Ya

    2014-01-01

    Femtosecond lasers have opened up new avenues in materials processing due to their unique characteristics of ultrashort pulse widths and extremely high peak intensities. One of the most important features of femtosecond laser processing is that a femtosecond laser beam can induce strong absorption in even transparent materials due to nonlinear multiphoton absorption. This makes it possible to directly create three-dimensional (3D) microfluidic structures in glass that are of great use for fabrication of biochips. For fabrication of the 3D microfluidic structures, two technical approaches are being attempted. One of them employs femtosecond laser-induced internal modification of glass followed by wet chemical etching using an acid solution (Femtosecond laser-assisted wet chemical etching), while the other one performs femtosecond laser 3D ablation of the glass in distilled water (liquid-assisted femtosecond laser drilling). This paper provides a review on these two techniques for fabrication of 3D micro and nanofluidic structures in glass based on our development and experimental results.

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

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  4. 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

  5. Velocity Measurement in Carotid Artery: Quantitative Comparison of Time-Resolved 3D Phase-Contrast MRI and Image-based Computational Fluid Dynamics

    PubMed Central

    Sarrami-Foroushani, Ali; Nasr Esfahany, Mohsen; Nasiraei Moghaddam, Abbas; Saligheh Rad, Hamidreza; Firouznia, Kavous; Shakiba, Madjid; Ghanaati, Hossein; Wilkinson, Iain David; Frangi, Alejandro Federico

    2015-01-01

    Background: Understanding hemodynamic environment in vessels is important for realizing the mechanisms leading to vascular pathologies. Objectives: Three-dimensional velocity vector field in carotid bifurcation is visualized using TR 3D phase-contrast magnetic resonance imaging (TR 3D PC MRI) and computational fluid dynamics (CFD). This study aimed to present a qualitative and quantitative comparison of the velocity vector field obtained by each technique. Subjects and Methods: MR imaging was performed on a 30-year old male normal subject. TR 3D PC MRI was performed on a 3 T scanner to measure velocity in carotid bifurcation. 3D anatomical model for CFD was created using images obtained from time-of-flight MR angiography. Velocity vector field in carotid bifurcation was predicted using CFD and PC MRI techniques. A statistical analysis was performed to assess the agreement between the two methods. Results: Although the main flow patterns were the same for the both techniques, CFD showed a greater resolution in mapping the secondary and circulating flows. Overall root mean square (RMS) errors for all the corresponding data points in PC MRI and CFD were 14.27% in peak systole and 12.91% in end diastole relative to maximum velocity measured at each cardiac phase. Bland-Altman plots showed a very good agreement between the two techniques. However, this study was not aimed to validate any of methods, instead, the consistency was assessed to accentuate the similarities and differences between Time-resolved PC MRI and CFD. Conclusion: Both techniques provided quantitatively consistent results of in vivo velocity vector fields in right internal carotid artery (RCA). PC MRI represented a good estimation of main flow patterns inside the vasculature, which seems to be acceptable for clinical use. However, limitations of each technique should be considered while interpreting results. PMID:26793288

  6. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  7. 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.

  8. a Multiple Data Set Joint Inversion Global 3d P-Velocity Model of the Earth's Crust and Mantle for Improved Seismic Event Location

    NASA Astrophysics Data System (ADS)

    Ballard, S.; Begnaud, M. L.; Hipp, J. R.; Chael, E. P.; Encarnacao, A.; Maceira, M.; Yang, X.; Young, C. J.; Phillips, W.

    2013-12-01

    SALSA3D is a global 3D P wave velocity model of the Earth's crust and mantle developed specifically to provide seismic event locations that are more accurate and more precise than are locations from 1D and 2.5D models. In this paper, we present the most recent version of our model, for the first time jointly derived from multiple types of data: body wave travel times, surface wave group velocities, and gravity. The latter two are added to provide information in areas with poor body wave coverage, and are down-weighted in areas where body wave coverage is good. To constrain the inversions, we invoked empirical relations among the density, S velocity, and P velocity. We demonstrate the ability of the new SALSA3D model to reduce mislocations and generate statistically robust uncertainty estimates for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth events. We obtain path-dependent travel time prediction uncertainties for our model by computing the full 3D model covariance matrix of our tomographic system and integrating the model slowness variance and covariance along paths of interest. This approach yields very low travel time prediction uncertainties for well-sampled paths through the Earth and higher uncertainties for paths that are poorly represented in the data set used to develop the model. While the calculation of path-dependent prediction uncertainties with this approach is computationally expensive, uncertainties can be pre-computed for a network of stations and stored in 3D lookup tables that can be quickly and efficiently interrogated using GeoTess software.

  9. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  10. 3D interactive model of lumbar spinal structures of anesthetic interest.

    PubMed

    Prats-Galino, Alberto; Reina, Miguel A; Mavar Haramija, Marija; Puigdellivol-Sánchez, Anna; Juanes Méndez, Juan A; De Andrés, José A

    2015-03-01

    A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information. PMID:25352014

  11. 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.

  12. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

  13. 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.

  14. 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.

  15. 3-D Waveguide Effects of Topographical Structural Variation on Full Waveform Propagation: 3-D Finite Difference Modeling Comparisons with Field Data From Yuma Proving Ground, Arizona

    NASA Astrophysics Data System (ADS)

    Anderson, T. S.; Miller, R.; Greenfield, R.; Fisk, D.

    2002-12-01

    The propagation of seismic waves through regions of complex topography is not thoroughly understood. Surface waves, are of particular interest, as they are large in amplitude and can characterize the source depth, magnitude, and frequency content. The amplitude and frequency content of seismic waves that propagate in regions with large topographical variations are affected by both the scattering and blockage of the wave energy. The ability to predict the 3-d scattering due to topography will improve the understanding of both regional scale surface wave magnitudes, and refine surface wave discriminants as well as at the local scale (<2 km ) where it will aid in the development of rule of thumb guide lines for array sensor placement for real time sensing technologies. Ideally, when validating the numerical accuracy of a propagation model against field data, the input geologic parameters would be known and thus eliminates geology as a source of error in the calculation. In March of 2001, Kansas Geological Survey (KGS) performed a detailed seismic site characterization at the Smart Weapons Test Range, Yuma Proving Ground, Arizona. The result of the KGS characterization study is a high-resolution 3-d model that is used in our seismic simulations. The velocities Vs, Vp are calculated by tomography and refraction, attenuation coefficients estimated from the surface wave and from p-waves and are provided in a model with attributes resolved in 3-d to 0.5 meters. In the present work, we present comparisons of synthetic data with seismic data collected at the Smart Weapons Test Range to benchmark the accuracy achieved in simulating 3-d wave propagation in the vicinity of a topographical anomaly (trench). Synthetic seismograms are generated using a 3-d 8th order staggered grid visco-elastic finite difference code that accounts for topography. The geologic model is based on the Yuma site characterization. The size of these calculations required use of the DoD High Performance

  16. Finding the displacement of wood structure in heritage building by 3D laser scanner

    NASA Astrophysics Data System (ADS)

    Lee, M. C.; Tsai, Y. L.; Wang, R. Z.; Lin, M. L.

    2015-08-01

    Heritage buildings are highly prone to long term damage from the microclimate, scourge and vandalism, which can result in damaged materials, structures, painting and cultural heritage items. This study will focus on finding the displacement of wood structural members through the use of a 3D laser scanner and the 4D concept of time. The results will compare the scans from different periods to find the difference (if any) in the structural member position. Wood structures usually consist of numerous wood members connected to form the structure. However, these members can be damaged in various ways such as physical mechanisms, chemical reactions, and biological corrosion. When damage to the wood structure occurs, the structural displacement can be affected, and if affected severely, can lead to a building collapse. Monitoring of the structural displacement is the best way to discover damage immediately and to preserve the heritage building. However, the Cultural Heritage Preservation Law in Taiwan prohibits the installation of monitoring instruments (e.g strain gauge, accelerometer) in historic structures (heritage buildings). Scanning the wood structure with 3D lasers is the most non-intrusive method and quickly achieves displacement through visualization. The displacement scan results can be compared with different periods and different members to analyze the severity of damage. Once the 3D scanner is installed, the whole building is scanned, and point clouds created to build the visual building model. The structural displacement can be checked via the building model and the differences are measured between each member to find the high risk damaged areas or members with large displacement. Early detection of structural damage is the most effective way means of preservation.

  17. The structure of Nevada`s Grant Canyon and Bacon Flat oil fields from 3-D seismic data

    SciTech Connect

    Johnson, E.H.; Zwart, D.W.

    1995-06-01

    The 20 million barrel Grant Canyon structure and its satellite feature, the one million barrel Bacon Flat field, are located at the eastern edge of Railroad Valley, Nevada. Utilizing an eleven square mile 3-D seismic survey, we have unraveled the complicated structure of the field area. The seismic data were calibrated to known geology with 21 wells drilled prior to the 1993 3-D survey, and 4 recent wells. The 3-D data cube provided vertical 2-D seismic lines every 60 feet. Horizontal slices of the data cube rendered {open_quotes}map views{close_quotes} of the structural trends. Still, the interpretation of this complex area was difficult, hampered by extreme velocity variations in the valley fill sediments that degraded data resolution and skewed the imaged structures. The Grant Canyon and Bacon Flat reservoirs are shown to be remnants of detached Devonian rocks that rest upon a northwest-trending salient of younger Paleozoic rocks. The Paleozoic rocks that form the salient are truncated to the southeast against the Troy Intrusive. Beneath the salient, the flank of the intrusive dips about 30 degrees northwest. We show Bacon Flat to be an isolated closure northwest of Grant Canyon field. However, on the south flank of the Grant Canyon reservoir, a significant oil accumulation was trapped on the down side of a normal fault, 400 feet low to the oil column of the field. This appears to be anomalous for a carbonate reservoir with extraordinary permeability, but suggests that more oil may be trapped in the area, on the flanks of producing structures.

  18. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  19. 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

  20. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  1. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  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 Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  4. Sequence-based identification of 3D structural modules in RNA with RMDetect.

    PubMed

    Cruz, José Almeida; Westhof, Eric

    2011-06-01

    Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data. PMID:21552257

  5. 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.

  6. Experimentation of structured light and stereo vision for underwater 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Bruno, F.; Bianco, G.; Muzzupappa, M.; Barone, S.; Razionale, A. V.

    Current research on underwater 3D imaging methods is mainly addressing long range applications like seafloor mapping or surveys of archeological sites and shipwrecks. Recently, there is an increasing need for more accessible and precise close-range 3D acquisition technologies in some application fields like, for example, monitoring the growth of coral reefs or reconstructing underwater archaeological pieces that in most cases cannot be recovered from the seabed. This paper presents the first results of a research project that aims to investigate the possibility of using active optical techniques for the whole-field 3D reconstructions in an underwater environment. In this work we have tested an optical technique, frequently used for in air acquisition, based on the projection of structured lighting patterns acquired by a stereo vision system. We describe the experimental setup used for the underwater tests, which were conducted in a water tank with different turbidity conditions. The tests have evidenced that the quality of 3D reconstruction is acceptable even with high turbidity values, despite the heavy presence of scattering and absorption effects.

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

    PubMed Central

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site. PMID:26257525

  9. 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.

  10. Topology optimization of 3D structures with design-dependent loads

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Liu, Shu-Tian; Zhang, Xiong

    2010-10-01

    Topology optimization of continuum structures with design-dependent loads has long been a challenge. In this paper, the topology optimization of 3D structures subjected to design-dependent loads is investigated. A boundary search scheme is proposed for 3D problems, by means of which the load surface can be identified effectively and efficiently, and the difficulties arising in other approaches can be overcome. The load surfaces are made up of the boundaries of finite elements and the loads can be directly applied to corresponding element nodes, which leads to great convenience in the application of this method. Finally, the effectiveness and efficiency of the proposed method is validated by several numerical examples.

  11. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    PubMed Central

    Vlachakis, Dimitrios; Champeris Tsaniras, Spyridon; Tsiliki, Georgia; Megalooikonomou, Vasileios; Kossida, Sophia

    2016-01-01

    Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electro-static surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

  12. 3D simulation of interdendritic flow through a Al-18wt.%Cu structure captured with X-ray microtomography

    NASA Astrophysics Data System (ADS)

    Domitner, J.; Hölzl, C.; Kharicha, A.; Wu, M.; Ludwig, A.; Köhler, M.; Ratke, L.

    2012-01-01

    A central parameter to describe the formation of porosity and macrosegregation during casting processes is the permeability of the dendritic mushy zone. To determine this specific feature for a binary Al-18wt.%Cu alloy, flow simulations based on the Lattice Boltz-mann (LB) method were performed. The LB method allows an efficient solving of fluid flow problems dealing with complex shapes within an acceptable period of time. The 3D structure required as input for the simulations was captured with X-ray microtomography, which enables the generation of representative geometries for permeability investigations. Removing the eutectic phase from the measured dataset generated a remaining network of solid primary dendrites. In the simulations, a pressure gradient was applied to force the liquid through the free interdendritic channels. The permeability of the structure was then calculated from the resulting flow velocity pattern using Darcy's law. To examine the influence of different boundary conditions on the results obtained, several simulations were conducted.

  13. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  15. 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.

  16. A theoretical study of the structure and stability of borohydride on 3d transition metals

    NASA Astrophysics Data System (ADS)

    Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

    2012-12-01

    The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

  17. Assessment of the isostatic state and the load distribution of the European Molasse basin by means of lithospheric-scale 3D structural and 3D gravity modelling

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    The European Molasse basin is a foreland basin situated at the northern front of the European Alps and has formed as a consequence of the Euro-Adriatic continental collision since the Tertiary. Today, it is underlain by Mesozoic sedimentary successions on top of a Paleozoic crust. To investigate the deep structure, the isostatic state, as well as the load distribution in the basin and the adjacent Alpine area, we constructed a lithospheric-scale 3D structural model by implementing available surface, well and seismic data. Subsequently, the structure of the model was constrained by means of 3D gravity modelling. Complementary, the isostatic state has been assessed based on the calculation of the 3D load distribution. Our results show that the Molasse basin is not in isostatic equilibrium and that the gravity field of the area is strongly controlled by the configuration of the crystalline crust. Furthermore, we show that the area is influenced by significant lateral load variations down to a depth of -150 km, which are considerably larger than commonly assumed for this level. Furthermore, our results allow a first-order assessment of the minimum compensating horizontal stress required to prevent gravitational collapse.

  18. Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

    NASA Astrophysics Data System (ADS)

    Qin, W.; Yang, L.

    2004-05-01

    Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

  19. The 3-D distribution of random velocity inhomogeneities in southwestern Japan and the western part of the Nankai subduction zone

    NASA Astrophysics Data System (ADS)

    Takahashi, Tsutomu; Obana, Koichiro; Yamamoto, Yojiro; Nakanishi, Ayako; Kodaira, Shuichi; Kaneda, Yoshiyuki

    2013-05-01

    waves at high frequencies (>1 Hz) show collapsed and broadened wave trains caused by multiple scattering in the lithosphere. This study analyzed the envelopes of direct S waves in southwestern Japan and on the western side of the Nankai trough and estimated the spatial distribution of random inhomogeneities by assuming a von Kármán type power spectral density function (PSDF). Strongly inhomogeneous media have been mostly imaged at shallow depth (0-20 km depth) in the onshore area of southwestern Japan, and their PSDF is represented as P(m) ≈ 0.05m-3.7 km3, with m being the spatial wave number, whereas most of the other area shows weak inhomogeneities of which PSDF is P(m) ≈ 0.005m-4.5 km3. At Hyuga-nada in Nankai trough, there is an anomaly of inhomogeneity of which PSDF is estimated as P(m) ≈ 0.01m-4.5 km3. This PSDF has the similar spectral gradient with the weakly inhomogeneous media, but has larger power spectral density than other offshore areas. This anomalous region is broadly located in the subducted Kyushu Palau ridge, which was identified by using velocity structures and bathymetry, and it shows no clear correlation with the fault zones of large earthquakes in past decades. These spatial correlations suggest that possible origins of inhomogeneities at Hyuga-nada are ancient volcanic activity in the oceanic plate or deformed structures due to the subduction of the Kyushu Palau ridge.

  20. 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.

  1. 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

  2. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

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

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences. PMID:23824509

  3. 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.

  4. 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.

  5. 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

  6. Integration of nano-scale components and supports in micromachined 3D silicon structures

    NASA Astrophysics Data System (ADS)

    Song, J.; Azimi, S.; Y Dang, Z.; Breese, M. B. H.

    2014-04-01

    We have developed a process for the three-dimensional (3D) machining of p-type silicon on a micro- and nano-scale using high-energy ion beam irradiation with one or more energies and fluences, followed by electrochemical anodization in hydrofluoric acid. We present a study of the dependence of our fabricated structures on irradiating ion energies, fluences, geometries and wafer resistivity. All these factors determine whether the micro- and nano-scale features are properly connected to the supports in the 3D silicon structures. If wrongly chosen, any of these factors may cause a breakage at the connection through localized over-etching. Under optimum irradiation and anodization conditions, free-standing patterned membranes can be fabricated with feature dimensions of 100 nm over areas of many square millimeters. This investigation is based on silicon structures but is relevant to any electro-assisted etching process for 3D fabrication, paving the way for achieving free-standing silicon photonics, mechanical resonators and micro-/nano-electromechanical systems.

  7. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    PubMed

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

  8. 3D shallow structures in the Baogutu area, Karamay, determined by eikonal tomography of short-period ambient noise surface waves

    NASA Astrophysics Data System (ADS)

    Xu, Hongrui; Luo, Yinhe; Chen, Chao; Xu, Yixian

    2016-06-01

    Eikonal tomography based on ambient noise data is one of the most effective methods to reveal shallow earth structures. By tracking surface wave phase fronts, constructing travel time surfaces, and computing the gradients of travel time surfaces to generate phase velocity maps, eikonal tomography avoids the ray tracing and matrix construction and inversion in the traditional surface wave tomography methods. In this study, we collect continuous ambient noise data recorded by a dense seismic array in Karamay, Xinjiang to construct a 3D model of shallow structures using eikonal tomography. The seismic array consists of 35 stations with shortest interstation distance close to 1 km. 890 empirical surface wave Green's functions (EGFs) between each station pair are retrieved by cross-correlating one or two months of continuous ambient noise data. From these EGFs, surface wave travel times in the frequency range of 1.8 to 4.0 Hz are measured by a frequency-time analysis technique (FTAN). Then, eikonal tomography is adopted to construct Rayleigh wave phase velocity maps and estimate the phase velocity uncertainties. Finally, we invert the obtained phase velocity dispersion curves for 1D shear velocity profiles and then assemble these 1D profiles to construct a 3D shear velocity model. Major velocity features of our 3D model are correlated well with the known geological features. A shallow east-west velocity discontinuity is observed, which clearly reflects the lithological change between Baogutu formation (C1b) and Xibeikulasi formation (C1x) of lower Carboniferous system. Low shear velocities are observed beneath the location of porphyry copper deposit (V), possibly related to stockwork fracture and hydrothermal brecciation developed during the intrusion of deep magma in forming the deposit.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  11. 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.

  12. 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).

  13. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm. PMID:24481593

  14. 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

  15. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  16. 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

  17. 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.

  18. 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

  19. 3D measurement method based on combined temporal encoding structured light

    NASA Astrophysics Data System (ADS)

    Yu, Xiaoyang; Wang, Yang; Yu, Shuang; Cheng, Hao; Sun, Xiaoming; Yu, Shuchun; Chen, Deyun

    2013-10-01

    Three-dimensional (3D) vision measurement technology based on encoding structured light plays an important role and has become the main development trend in the field of 3D non-contact measurement. However, how to synthetically improve measurement speed, accuracy and sampling density is still a difficult problem. Thus in the present work, a novel 3D measurement method based on temporal encoding structured light by combining trapezoidal phase-shifting pattern and cyclic code pattern is proposed. Due to trapezoidal phase-shifting has the advantages of high sampling density and high-speed, the proposed method can maintain these advantages by using cyclic code to expand the range of trapezoidal phase-shifting. In addition, the correction scheme is designed to solve the problem of cycle dislocation. Finally, simulation experimental platform is built with 3ds max and MATLAB. Experimental analyses and results show that, the maximal error is less than 3 mm in the range from 400 mm to 1100 mm, cycle dislocation correction has a good effect.

  20. 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.

  1. An unprecedented 3D POM-Ag architecture with intertwined and homological helical structures.

    PubMed

    Sha, Jing-Quan; Li, Meng-Ting; Sun, Jing-Wen; Zhang, Yu-Nan; Yan, Peng-Fei; Li, Guang-Ming

    2013-06-01

    A new hybrid compound, Na[Ag6(pyttz)2(H2O)][PMo12O40] (pyttz = 3-(pyrid-3-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl), has been hydrothermally synthesized and structurally characterized by routine techniques. X-ray diffraction analysis reveals that the title compound is constructed by the 2D Ag-pyttz coordination polymer and 3D Ag-POM architecture with helix. A fascinating structural feature is the assembling fashion of the right- and left-helical chain, namely, the helical chains with different orientations are intertwined with each other forming intertwined double helical layers along the c-axis, and the identical left- or right-handed helical chains are fused together in a hand-by-hand mode generating another homological helical layer along the a-axis. As a result, these helical layers intersect each other obtaining an unprecedented 3D POM-Ag inorganic architecture. Note that the 3D framework with a helix constructed by POMs and metal ions has never been observed up to date. Additionally, its photocatalytic degradation of RhB was also investigated. PMID:23558903

  2. Direct observation in 3d of structural crossover in binary hard sphere mixtures

    NASA Astrophysics Data System (ADS)

    Statt, Antonia; Pinchaipat, Rattachai; Turci, Francesco; Evans, Robert; Royall, C. Patrick

    2016-04-01

    For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon et al., J. Chem. Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl et al., Phys. Rev. Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.

  3. 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.

  4. 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

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

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  6. 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

    Knowledge on the ability of fluids to infiltrate subsurface rocks is of major importance for underground constructions, geothermal or radioactive waste disposal projects. In this study, we focus on the characterization of water infiltration pathways, their 3D geometries and origins. Based on surface and subsurface mapping in combination with drill core data, we developed by the use of MoveTM (Midland Valley Exploration Ltd.) a 3D structural model of the Grimsel Test Site (GTS). GTS is an underground laboratory operated by NAGRA, the Swiss organisation responsible for the management of nuclear waste. It is located within a suite of post-Variscan magmatic bodies comprising former granitic and granodioritic melts, which are dissected by mafic and aplitic dikes. During Alpine orogeny, the suite was tectonically overprinted within two stages of ductile deformation (Wehrens et al., in prep.) followed by brittle overprint of some of the shear zones during the retrograde exhumation history. It is this brittle deformation, which controls today's water infiltration network. However, the associated fractures, cataclasites and fault gouges are controlled themselves by aforementioned pre-existing mechanical discontinuities, whose origin ranges back as far as to the magmatic stage. For example, two sets of vertically oriented mafic dikes (E-W and NW-SE striking) and compositional heterogeneities induced by magmatic segregation processes in the plutonic host rocks served as nucleation sites for Alpine strain localization. Subsequently, NE-SW, E-W and NW-SE striking ductile shear zones were formed, in combination with high temperature fracturing while dissecting the host rocks in a complex 3D pattern (Wehrens et al, in prep.). Whether the ductile shear zones have been subjected to brittle reactivation and can serve as infiltration pathways or not, depends strongly on their orientations with respect to the principal stress field. Especially where deformation structures intersect

  7. Reconstruction of 3D structure using stochastic methods: morphology and transport properties

    NASA Astrophysics Data System (ADS)

    Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena

    2013-04-01

    One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions

  8. 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.

  9. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

    PubMed Central

    Gouet, Patrice; Robert, Xavier; Courcelle, Emmanuel

    2003-01-01

    The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Cα trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript. PMID:12824317

  10. The "lnc" between 3D chromatin structure and X chromosome inactivation.

    PubMed

    Pandya-Jones, Amy; Plath, Kathrin

    2016-08-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  11. A 3D moisture-stress FEM analysis for time dependent problems in timber structures

    NASA Astrophysics Data System (ADS)

    Fortino, Stefania; Mirianon, Florian; Toratti, Tomi

    2009-11-01

    This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.

  12. 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

  13. 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

  14. The 3D pore structure and fluid dynamics simulation of macroporous monoliths: High permeability due to alternating channel width.

    PubMed

    Jungreuthmayer, Christian; Steppert, Petra; Sekot, Gerhard; Zankel, Armin; Reingruber, Herbert; Zanghellini, Jürgen; Jungbauer, Alois

    2015-12-18

    Polymethacrylate-based monoliths have excellent flow properties. Flow in the wide channel interconnected with narrow channels is theoretically assumed to account for favorable permeability. Monoliths were cut into 898 slices in 50nm distances and visualized by serial block face scanning electron microscopy (SBEM). A 3D structure was reconstructed and used for the calculation of flow profiles within the monolith and for calculation of pressure drop and permeability by computational fluid dynamics (CFD). The calculated and measured permeabilities showed good agreement. Small channels clearly flowed into wide and wide into small channels in a repetitive manner which supported the hypothesis describing the favorable flow properties of these materials. This alternating property is also reflected in the streamline