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Sample records for detailed structural characterization

  1. Detailed Structural Characterization of Unbound Protein Phosphatase 1 Inhibitors

    PubMed Central

    Dancheck, Barbara; Nairn, Angus C.; Peti, Wolfgang

    2009-01-01

    Protein Phosphatase 1 (PP1) is an essential and ubiquitous serine/threonine protein phosphatase that is regulated by more than 100 known inhibitor and targeting proteins. It is currently unclear how protein inhibitors distinctly and specifically regulate PP1 to enable rapid responses to cellular alterations. We demonstrate that two PP1 inhibitors, I-2 and DARPP-32, belong to the class of intrinsically unstructured proteins (IUPs). We show that both inhibitors have distinct preferences for transient local and long range structure. These preferences are likely their structural signature for their interaction with PP1. Furthermore, we show that upon phosphorylation of Thr34 in DARPP-32, which turns DARPP-32 into a potent inhibitor of PP1, neither local nor long range structure of DARPP-32 is altered. Therefore, our data suggests a role for these transient 3-dimensional topologies in binding mechanisms that enable extensive contacts with PP1's invariant surfaces. Together, these interactions enable potent and selective inhibition of PP1. PMID:18954090

  2. Mass Spectrometric Characterization of Protein Structure Details Refines the Proteome Signature for Invasive Ductal Breast Carcinoma

    NASA Astrophysics Data System (ADS)

    Röwer, Claudia; Koy, Cornelia; Hecker, Michael; Reimer, Toralf; Gerber, Bernd; Thiesen, Hans-Jürgen; Glocker, Michael O.

    2011-03-01

    Early diagnosis as well as individualized therapies are necessary to reduce the mortality of breast cancer, and personalized patient care strategies rely on novel prognostic or predictive factors. In this study, with six breast cancer patients, 2D gel analysis was applied for studying protein expression differences in order to distinguish invasive ductal breast carcinoma, the most frequent breast tumor subtype, from control samples. In total, 1203 protein spots were assembled in a 2D reference gel. Differentially abundant spots were subjected to peptide mass fingerprinting for protein identification. Twenty proteins with their corresponding 38 differentially expressed 2D gel spots were contained in our previously reported proteome signature, suggesting that distinct protein forms were contributing. In-depth MS/MS measurements enabled analyses of protein structure details of selected proteins. In protein spots that significantly contributed to our signature, we found that glyceraldehyde-3-phosphate dehydrogenase was N-terminally truncated, pyruvate kinase M2 and nucleoside diphosphate kinase A but not other isoforms of these proteins were of importance, and nucleophosmin phosphorylation at serine residues 106 and 125 were clearly identified. Principle component analysis and hierarchical clustering with normalized quantitative data from the 38 spots resulted in accurate separation of tumor from control samples. Thus, separation of tissue samples as in our initial proteome signature could be confirmed even with a different proteome analysis platform. In addition, detailed protein structure investigations enabled refining our proteome signature for invasive ductal breast carcinoma, opening the way to structure-/function studies with respect to disease processes and/or therapeutic intervention.

  3. Review of Ship Structural Details

    DTIC Science & Technology

    1977-01-01

    8 4.3 Knee and Beam Brackets 4-11 4.3.1 Brackets for Girders and Deep Webs 4-11 4.3.2 Brackets Connecting Rolled Sections 4-15 4.4 Tripping...are shell stringers penetrating deep web frames and longitudinal girders penetrating deep transverses. This is not a common detail. If double...34. 3-76 ^"SECTION ’’.’(-K PLAJ iNG * S v *^ 4Fb^:TH»r.KNF.^ SAME AS FLAMGE ► BULKHFADQR DEEP WEB SS- 9 Detail Type: STANCHION END

  4. Aircraft wing structure detail design

    NASA Technical Reports Server (NTRS)

    Sager, Garrett L.; Roberts, Ron; Mallon, Bob; Alameri, Mohamed; Steinbach, Bill

    1993-01-01

    The provisions of this project call for the design of the structure of the wing and carry-through structure for the Viper primary trainer, which is to be certified as a utility category trainer under FAR part 23. The specific items to be designed in this statement of work were Front Spar, Rear Spar, Aileron Structure, Wing Skin, and Fuselage Carry-through Structure. In the design of these parts, provisions for the fuel system, electrical system, and control routing were required. Also, the total weight of the entire wing planform could not exceed 216 lbs. Since this aircraft is to be used as a primary trainer, and the SOW requires a useful life of 107 cycles, it was decided that all of the principle stresses in the structural members would be kept below 10 ksi. The only drawback to this approach is a weight penalty.

  5. Detailed Aerosol Characterization using Polarimetric Measurements

    NASA Astrophysics Data System (ADS)

    Hasekamp, Otto; di Noia, Antonio; Stap, Arjen; Rietjens, Jeroen; Smit, Martijn; van Harten, Gerard; Snik, Frans

    2016-04-01

    Anthropogenic aerosols are believed to cause the second most important anthropogenic forcing of climate change after greenhouse gases. In contrast to the climate effect of greenhouse gases, which is understood relatively well, the negative forcing (cooling effect) caused by aerosols represents the largest reported uncertainty in the most recent assessment of the International Panel on Climate Change (IPCC). To reduce the large uncertainty on the aerosol effects on cloud formation and climate, accurate satellite measurements of aerosol optical properties (optical thickness, single scattering albedo, phase function) and microphysical properties (size distribution, refractive index, shape) are essential. There is growing consensus in the aerosol remote sensing community that multi-angle measurements of intensity and polarization are essential to unambiguously determine all relevant aerosol properties. This presentations adresses the different aspects of polarimetric remote sensing of atmospheric aerosols, including retrieval algorithm development, validation, and data needs for climate and air quality applications. During past years, at SRON-Netherlands Instite for Space Research retrieval algorithms have been developed that make full use of the capabilities of polarimetric measurements. We will show results of detailed aerosol properties from ground-based- (groundSPEX), airborne- (NASA Research Scanning Polarimeter), and satellite (POLDER) measurements. Also we will discuss observational needs for future instrumentation in order to improve our understanding of the role of aerosols in climate change and air quality.

  6. SU-E-T-170: Characterization of the Location, Extent, and Proximity to Critical Structures of Target Volumes Provides Detail for Improved Outcome Predictions Among Pancreatic Cancer Patients

    SciTech Connect

    Cheng, Z; Moore, J; Rosati, L; Mian, O; Narang, A; Herman, J; McNutt, T

    2015-06-15

    Purpose: In radiotherapy, size, location and proximity of the target to critical structures influence treatment decisions. It has been shown that proximity of the target predicts dosimetric sparing of critical structures. In addition to dosimetry, precise location of disease has further implications such as tumor invasion, or proximity to major arteries that inhibit surgery. Knowledge of which patients can be converted to surgical candidates by radiation may have high impact on future treat/no-treat decisions. We propose a method to improve our characterization of the location of pancreatic cancer and treatment volume extent with respect to nearby arteries with the goal of developing features to improve clinical predictions and decisions. Methods: Oncospace is a local learning health system that systematically captures clinical outcomes and all aspects of radiotherapy treatment plans, including overlap volume histograms (OVH) – a measure of spatial relationships between two structures. Minimum and maximum distances of PTV and OARs based on OVH, PTV volume, anatomic location by ICD-9 code, and surgical outcome were queried. Normalized distance to center from the left and right kidney was calculated to indicate tumor location and laterality. Distance to critical arteries (celiac, superior mesenteric, common hepatic) is validated by surgical status (borderline resectable, locally advanced converted to resectable). Results: There were 205 pancreas stereotactic body radiotherapy patients treated from 2009–2015 queried. Location/laterality of tumor based on kidney OVH show strong trends between location by OVH and by ICD-9. Compared to the locally advanced group, the borderline resectable group showed larger geometrical distance from critical arteries (p=0.03). Conclusion: Our platform enabled analysis of shape/size-location relationships. These data suggest that PTV volume and attention to distance between PTVs and surrounding OARs and major arteries may be

  7. Structural details, pathways, and energetics of unfolding apomyoglobin.

    PubMed

    Onufriev, Alexey; Case, David A; Bashford, Donald

    2003-01-17

    Protein folding is often difficult to characterize experimentally because of the transience of intermediate states, and the complexity of the protein-solvent system. Atomistic simulations, which could provide more detailed information, have had to employ highly simplified models or high temperatures, to cope with the long time scales of unfolding; direct simulation of folding is even more problematic. We report a fully atomistic simulation of the acid-induced unfolding of apomyoglobin in which the protonation of acidic side-chains to simulate low pH is sufficient to induce unfolding at room temperature with no added biasing forces or other unusual conditions; and the trajectory is validated by comparison to experimental characterization of intermediate states. Novel insights provided by their analysis include: characterization of a dry swollen globule state forming a barrier to initial unfolding or final folding; observation of cooperativity in secondary and tertiary structure formation and its explanation in terms of dielectric environments; and structural details of the intermediate and the completely unfolded states. These insights involve time scales and levels of structural detail that are presently beyond the range of experiment, but come within reach through the simulation methods described here. An implicit solvation model is used to analyze the energetics of protein folding at various pH and ionic strength values, and a reasonable estimate of folding free energy is obtained. Electrostatic interactions are found to disfavor folding.

  8. Structural details of the glycosyltransferase step of peptidoglycan assembly.

    PubMed

    Lovering, Andrew L; Gretes, Michael; Strynadka, Natalie C J

    2008-10-01

    The importance of peptidoglycan in forming the basis of the bacterial cell wall has led to many studies investigating its synthesis. The step of cross-linkage via transpeptidation, and its inhibition by penicillins, has been extremely well characterized yet knowledge of the preceding glycosyltransfer reaction remained elusive until recently. The structures of two glycosyltransferase enzymes, catalyzing membrane-based polymerization of the lipid II monomer unit, have presented a means of elucidating the molecular details of this highly desirable antibiotic target. Evidence acquired before the publication of the structures is related here to these new findings, with particular emphasis on the recognition of substrates and inhibitors.

  9. Results of Detailed Hydrologic Characterization Tests - Fiscal Year 2000

    SciTech Connect

    Spane, Frank A.; Thorne, Paul D.; Newcomer, Darrell R.

    2001-05-15

    This report provides the resluts of detailed hydrologic characterization tests conducted within eleven Hanford Site wells during fiscal year 2000. Detailed characterization tests performed included groundwater-flow characterization; barometric response evaluation; slug tests; single-well tracer tests; constant-rate pumping tests; and in-well, vertical flow tests. Hydraulic property estimates obtained from the detailed hydrologic tests include transmissivity; hydraulic conductivity; specific yield; effective porosity; in-well, lateral flow velocity; aquifer-flow velocity; vertical distribution of hydraulic conductivity (within the well-screen section); and in-well, verticla flow velocity. In addition, local groundwater-flow characteristics (i.e., hydraulic gradient and flow direction) were determined for four sites where detailed well testing was performed.

  10. Results of Detailed Hydrologic Characterization Tests - Fiscal Year 1999

    SciTech Connect

    Spane, Frank A.; Thorne, Paul D.; Newcomer, Darrell R.

    2001-01-19

    This report provides the results of detailed hydrologic characterization tests conducted within newly constructed Hanford Site wells during FY 1999. Detailed characterization tests performed during FY 1999 included: groundwater flow characterization, barometric response evaluation, slug tests, single-well tracer tests, constant-rate pumping tests, and in-well vertical flow tests. Hydraulic property estimates obtained from the detailed hydrologic tests include: transmissivity, hydraulic conductivity, specific yield, effective porosity, in-well lateral flow velocity, aquifer flow velocity, vertical distribution of hydraulic conductivity (within the well-screen section) and in-well vertical flow velocity. In addition, local groundwater flow characteristics (i.e., hydraulic gradient and flow direction) were determined for four sites where detailed well testing was performed.

  11. Structural concepts and details for seismic design

    SciTech Connect

    Not Available

    1991-09-01

    This manual discusses building and building component behavior during earthquakes, and provides suggested details for seismic resistance which have shown by experience to provide adequate performance during earthquakes. Special design and construction practices are also described which, although they might be common in some high-seismic regions, may not be common in low and moderate seismic-hazard regions of the United States. Special attention is given to describing the level of detailing appropriate for each seismic region. The UBC seismic criteria for all seismic zones is carefully examined, and many examples of connection details are given. The general scope of discussion is limited to materials and construction types common to Department of Energy (DOE) sites. Although the manual is primarily written for professional engineers engaged in performing seismic-resistant design for DOE facilities, the first two chapters, plus the introductory sections of succeeding chapters, contain descriptions which are also directed toward project engineers who authorize, review, or supervise the design and construction of DOE facilities. 88 refs., 188 figs.

  12. Structured detailed opto-mechanical tolerance modeling

    NASA Astrophysics Data System (ADS)

    Swart, P. C.

    2016-02-01

    Opto-mechanical tolerancing is a complex art, which is often reduced to inadequate tabled data of allowable tilts and decentres. During the process the respective roles of optical- and mechanical designers can become entangled and a source of conflict. A framework of principles is introduced to guide the design team through these murky waters. From these principles the development of a catalogue of models, practices and past precedents are proposed. An example is presented to serve as illustration. The final result is a model, of opto-mechanical tolerances, which allows a structured flow of tolerances into optical performance prediction.

  13. Interior detail of structural elements section; camera facing east. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior detail of structural elements section; camera facing east. - Mare Island Naval Shipyard, Supply Building, Walnut Avenue, southeast corner of Walnut Avenue & Fifth Street, Vallejo, Solano County, CA

  14. Structural details below roadway, looking north from south abutment. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Structural details below roadway, looking north from south abutment. - Pleasantville Covered Bridge, Spanning Little Manatawny Creek at Covered Bridge Road (State Route 1030), Manatawny, Berks County, PA

  15. Fatigue Characterization of Fabricated Ship Details. Phase 2

    DTIC Science & Technology

    1988-05-01

    structural weldments are evi- dent in Fig 1-1 which shows the structural details covered in the AISC fa- tigue provisions [1-11. 1.2 The Fatigue Design of...reliability: see Fig. 1-9. 1.6 References 1-1. AISC . "Specification for the Design, Fabrication and Erection of Structural Steel for Buildings," American...Tensile Chemistry (%) Description Thickness Strength Strength C,(a) Mn P S (mm) MPa (ksi) MPa (ksi) ASTM A131 234 Min. 400 to 489 .23,(b) (c) . 05 . 05 Gr. A

  16. INTERIOR; DETAIL OF ROOF FRAMING STRUCTURE, LOOKING SOUTHWEST. Naval ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    INTERIOR; DETAIL OF ROOF FRAMING STRUCTURE, LOOKING SOUTHWEST. - Naval Computer & Telecommunications Area Master Station, Eastern Pacific, Radio Transmitter Facility Lualualei, Helix House No. 2, Base of Radio Antenna Structure No. 427, Makaha, Honolulu County, HI

  17. 31. View southeast from north side of structure noting detail ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    31. View southeast from north side of structure noting detail of Section 2 of the Metal Bent portion of the structure. - Augustine Bridge, Brandywine River,Augustine Cutoff, Wilmington, New Castle County, DE

  18. 8. Interior of Building 1015 (land plane hangar), structural detail, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Interior of Building 1015 (land plane hangar), structural detail, looking northeast - Naval Air Station Chase Field, Building 1015, Byrd Street, .82 mile South-southeast of intersection of Texas State Highway 202 & Independence Street, Beeville, Bee County, TX

  19. 7. Interior of Building 1015 (land plane hangar), structural detail, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. Interior of Building 1015 (land plane hangar), structural detail, looking northeast - Naval Air Station Chase Field, Building 1015, Byrd Street, .82 mile South-southeast of intersection of Texas State Highway 202 & Independence Street, Beeville, Bee County, TX

  20. 12. Exterior detail view of roof structure at eave, showing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. Exterior detail view of roof structure at eave, showing exposed rafter tails, skip sheathing and gutter - American Railway Express Company Freight Building, 1060 Northeast Division Street, Bend, Deschutes County, OR

  1. 18. DETAIL VIEW SHOWING SAWTOOTH MONITOR ROOF AND TYPICAL STRUCTURAL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. DETAIL VIEW SHOWING SAWTOOTH MONITOR ROOF AND TYPICAL STRUCTURAL CONFIGURATION OF TOP STORY, NORTH SECTION, THIRD FLOOR, LOOKING WEST INTO SOUTH SECTION - Massachusetts Mills, Cloth Room-Section 15, 95 Bridge Street, Lowell, Middlesex County, MA

  2. 9. Detail of viaduct's structural system with cattle pens beneath. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Detail of viaduct's structural system with cattle pens beneath. View to northeast. - South Omaha Union Stock Yards, Buckingham Road Viaduct, Twenty-ninth Street spanning Stockyard Cattle Pens, Omaha, Douglas County, NE

  3. 11. Detail, southeast corner, showing decorative elements of main structure, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. Detail, southeast corner, showing decorative elements of main structure, and window at the second story of the hose tower. - Independent Hose Company No. 3, Nineteenth & Belmont Streets, Bellaire, Belmont County, OH

  4. 16. DETAIL VIEW OF TYPICAL STRUCTURAL ELEMENTS; CROSSBAY 3 BETWEEN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    16. DETAIL VIEW OF TYPICAL STRUCTURAL ELEMENTS; CROSSBAY 3 BETWEEN D & E BAYS; LOOKING WSW. (Ryan) - Watervliet Arsenal, Building No. 135, Gillespie Road, South of Parker Road, Watervliet, Albany County, NY

  5. 18. DETAIL VIEW OF THE HIGH BAY STRUCTURAL SYSTEM AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. DETAIL VIEW OF THE HIGH BAY STRUCTURAL SYSTEM AND WINDOW ILLUMINATION AT THE SHRINK PIT AREA, S END OF B BAY; LOOKING SSE. (Ceronie) - Watervliet Arsenal, Building No. 135, Gillespie Road, South of Parker Road, Watervliet, Albany County, NY

  6. 4. DETAIL VIEW OF CROSS SECTION OF STRUCTURE, SHOWING EXTERIOR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. DETAIL VIEW OF CROSS SECTION OF STRUCTURE, SHOWING EXTERIOR FACINGS LINED WITH RUBBLE BACKING AND EARTH INFILL, LOOKING EAST - Rock Wall, North side of Battle Creek Canyon, Shingletown, Shasta County, CA

  7. 14. Detail, crack evidencing structural failure, northeast rear, view to ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. Detail, crack evidencing structural failure, northeast rear, view to southwest, 90mm lens. Note failure of sandstone lintel above window. - Benicia Arsenal, Powder Magazine No. 5, Junction of Interstate Highways 680 & 780, Benicia, Solano County, CA

  8. 15. Detail, cracks evidencing structural failure, northeast rear, view to ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    15. Detail, cracks evidencing structural failure, northeast rear, view to southwest, 90mm lens. - Benicia Arsenal, Powder Magazine No. 5, Junction of Interstate Highways 680 & 780, Benicia, Solano County, CA

  9. 22. Detail taken from center of bridge showing upper structure ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. Detail taken from center of bridge showing upper structure and roadway, from northwest. - Brady Street Bridge, Spanning Monongahela River at South Twenty-second Street, Pittsburgh, Allegheny County, PA

  10. 32. DETAIL OF BRIDGE COUNTERWEIGHTS AND SUSPENSION STRUCTURE BETWEEN BRIDGE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    32. DETAIL OF BRIDGE COUNTERWEIGHTS AND SUSPENSION STRUCTURE BETWEEN BRIDGE NOS. 12 AND 13. LOOKING EAST-SOUTHEAST. - Greenville Yard, Transfer Bridge System, Port of New York/New Jersey, Upper New York Bay, Jersey City, Hudson County, NJ

  11. 30. DETAIL OF COLLAPSED BRIDGE NO. 14 SUSPENSION STRUCTURE. LOOKING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    30. DETAIL OF COLLAPSED BRIDGE NO. 14 SUSPENSION STRUCTURE. LOOKING SOUTHWEST. - Greenville Yard, Transfer Bridge System, Port of New York/New Jersey, Upper New York Bay, Jersey City, Hudson County, NJ

  12. 91. Virginia Route 608 grade separation structure. Detail of the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    91. Virginia Route 608 grade separation structure. Detail of the scored wing walls and T beams. Looking southeast. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  13. 6. DETAIL OF DRIVE TRUCK ASSEMBLY. MOBILE SERVICE STRUCTURE SPANNING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. DETAIL OF DRIVE TRUCK ASSEMBLY. MOBILE SERVICE STRUCTURE SPANNING LAUNCHER BUILDING WITH FLAME DUCT FAR RIGHT; VIEW TO NORTHWEST. - Cape Canaveral Air Station, Launch Complex 17, Facility 28416, East end of Lighthouse Road, Cape Canaveral, Brevard County, FL

  14. 2. DETAIL OF STRUCTURAL SYSTEM FOR CANTILEVERED HOG RUN; BUILDING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. DETAIL OF STRUCTURAL SYSTEM FOR CANTILEVERED HOG RUN; BUILDING 168 (1960 HOG KILL) IS BENEATH HOG RUN - Rath Packing Company, Cantilevered Hog Run, Sycamore Street between Elm & Eighteenth Streets, Waterloo, Black Hawk County, IA

  15. Visitor center flight room, detail of twin structural piers at ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Visitor center flight room, detail of twin structural piers at northeast corner supporting flight room dome - Wright Brothers National Memorial Visitor Center, Highway 158, Kill Devil Hills, Dare County, NC

  16. 35. MISCELLANEOUS ARCHITECTURAL AND STRUCTURAL DETAILS. INEEL DRAWING NUMBER 200063300287106359. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    35. MISCELLANEOUS ARCHITECTURAL AND STRUCTURAL DETAILS. INEEL DRAWING NUMBER 200-0633-00-287-106359. FLUOR NUMBER 5775-CPP-633-A-9. - Idaho National Engineering Laboratory, Old Waste Calcining Facility, Scoville, Butte County, ID

  17. Interior detail of third level structural elements at south end; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior detail of third level structural elements at south end; camera facing west. - Mare Island Naval Shipyard, Supply Building, Walnut Avenue, southeast corner of Walnut Avenue & Fifth Street, Vallejo, Solano County, CA

  18. 6. DETAILED INTERIOR VIEW OF SOUTH SECTION, SHOWING ROOF STRUCTURAL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. DETAILED INTERIOR VIEW OF SOUTH SECTION, SHOWING ROOF STRUCTURAL SYSTEM, LOOKING NORTH AND UP - Marvine Colliery, Oil House, West side Boulevard Avenue, between East Parker Street & Route 380, Scranton, Lackawanna County, PA

  19. Detail of the wharf support structure with four pipes running ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of the wharf support structure with four pipes running across - U.S. Naval Base, Pearl Harbor, Marine Railway No. 2, Crane Wharf, Near intersection of Avenue G & Third Street , Pearl City, Honolulu County, HI

  20. INTERIOR VIEW, DETAIL OF BARREL ROOF STRUCTURE, FACING NORTHEAST. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    INTERIOR VIEW, DETAIL OF BARREL ROOF STRUCTURE, FACING NORTHEAST. - Southern Branch of the National Home for Disabled Volunteer Soldiers, Building 13, Harris Avenue at its intersection of Black Avenue and Woodfin Street, Hampton, Hampton, VA

  1. 6. Detail of heavy timber structural system at ground floor ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Detail of heavy timber structural system at ground floor level of Tender Frame Shop. - Central of Georgia Railway, Savannah Repair Shops & Terminal Facilities, Tender Frame Shop, Bounded by West Broad, Jones, West Boundary & Hull Streets, Savannah, Chatham County, GA

  2. 12. DETAIL VIEW OF STRUCTURE, FROM BELOW. VIEW OF THE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. DETAIL VIEW OF STRUCTURE, FROM BELOW. VIEW OF THE PARKER-MAYBERRY BRIDGE AND PART OF THE STRUCTURE OF THE COLORADO STREET BRIDGE, SEEN FROM THE ARROYO SECO BELOW THE COLORADO STREET BRIDGE - Colorado Street Bridge, Spanning Arroyo Seco at Colorado Boulevard, Pasadena, Los Angeles County, CA

  3. Battery Berry Observation Station, detail, frame structure meeting older masonry ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Battery Berry Observation Station, detail, frame structure meeting older masonry building on west side of structure; view east - Fort McKinley, Battery Berry Observation Station, North side of Wood Side Drive approximately 80 feet east of Spring Cove Lane, Great Diamond Island, Portland, Cumberland County, ME

  4. DETAIL VIEW OF THE STRUCTURE OF THE BASE OF THE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    DETAIL VIEW OF THE STRUCTURE OF THE BASE OF THE TEST STAND AND THE TAIL SECTION OF A REDSTONE (JUPITER) ROCKET. NOTE THE FLAME DEFLECTOR BEHIND THE STRUCTURE IN THE FOREGROUND. - Marshall Space Flight Center, Redstone Rocket (Missile) Test Stand, Dodd Road, Huntsville, Madison County, AL

  5. Detailed characterization of welding fumes in personal exposure samples

    NASA Astrophysics Data System (ADS)

    Quémerais, B.; Mino, James; Amin, M. R.; Golshahi, H.; Izadi, H.

    2015-05-01

    The objective of the project was to develop a method allowing for detailed characterization of welding particles including particle number concentration, size distribution, surface chemistry and chemical composition of individual particles, as well as metal concentration of various welding fumes in personal exposure samples using regular sampling equipment. A sample strategy was developed to evaluate the variation of the collection methods on mass concentration. Samples were collected with various samplers and filters at two different locations using our collection system. The first location was using a robotic welding system while the second was manual welding. Collected samples were analysed for mass concentration using gravimetryand metal concentration using ICP/OES. More advanced analysis was performed on selected filters using X-Ray Photoelectron Spectroscopy to determine surface composition of the particles, and X-Ray Diffraction to determine chemical composition of the fumes. Results showed that the robotic system had a lot of variation in space when the collection system was located close to the weld. Collection efficiency was found to be quite variable depending upon the type of filter. As well, metal concentrations in blank filters were dependent upon the type of filter with MCE presenting with the highest blank values. Results obtained with the XRD and XPS systems showed that it was possible to analyse a small of powdered welding fume sample but results on filters were not conclusive.

  6. Towards a detailed anthropometric body characterization using the Microsoft Kinect.

    PubMed

    Domingues, Ana; Barbosa, Filipa; Pereira, Eduardo M; Santos, Márcio Borgonovo; Seixas, Adérito; Vilas-Boas, João; Gabriel, Joaquim; Vardasca, Ricardo

    2016-01-01

    Anthropometry has been widely used in different fields, providing relevant information for medicine, ergonomics and biometric applications. However, the existent solutions present marked disadvantages, reducing the employment of this type of evaluation. Studies have been conducted in order to easily determine anthropometric measures considering data provided by low-cost sensors, such as the Microsoft Kinect. In this work, a methodology is proposed and implemented for estimating anthropometric measures considering the information acquired with this sensor. The measures obtained with this method were compared with the ones from a validation system, Qualisys. Comparing the relative errors determined with state-of-art references, for some of the estimated measures, lower errors were verified and a more complete characterization of the whole body structure was achieved.

  7. 5. STANDPIPE STRUCTURE DETAIL SHOWING CONNECTIONS TO PENSTOCKS, RIVETED SECTIONAL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. STANDPIPE STRUCTURE DETAIL SHOWING CONNECTIONS TO PENSTOCKS, RIVETED SECTIONAL CONSTRUCTION OF TWO OF THE THREE ORIGINAL STANDPIPES (PHOTO RIGHT), WELDED SECTIONAL CONSTRUCTION OF FOURTH STANDPIPE, AND MODERN VENTILATION VALVES ON FIFTH PENSTOCK AT PHOTO LEFT CENTER BETWEEN FOURTH STANDPIPE AND ORIGINAL TWO. VIEW TO NORTHEAST. - Big Creek Hydroelectric System, Powerhouse 3 Penstock Standpipes, Big Creek, Big Creek, Fresno County, CA

  8. 31. Detail of Southeast Light lens and roof structure of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    31. Detail of Southeast Light lens and roof structure of light gallery, 1985. Taken day after Hurricane Gloria, courtesy of Gerald F. Abbott and Block Island Historical Society. - Block Island Southeast Light, Spring Street & Mohegan Trail at Mohegan Bluffs, New Shoreham, Washington County, RI

  9. Detail of array structural elements through axis of array, looking ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of array structural elements through axis of array, looking north-northeast - Over-the-Horizon Backscatter Radar Network, Columbia Falls Radar Site Receive Sector Two Antenna Array, At the end of Shadagee Ridge Road, Columbia Falls, Washington County, ME

  10. 52. INTERIOR OF BRIDGE SUSPENSION STRUCTURE AND DETAIL OF LIFTING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    52. INTERIOR OF BRIDGE SUSPENSION STRUCTURE AND DETAIL OF LIFTING SCREW MACHINERY ABOVE BRIDGE NOS. 12 AND 11. LOOKING NORTH. - Greenville Yard, Transfer Bridge System, Port of New York/New Jersey, Upper New York Bay, Jersey City, Hudson County, NJ

  11. Interior detail of the north side roof structure and windows ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior detail of the north side roof structure and windows in the sail loft. View facing east northeast - U.S. Naval Base, Pearl Harbor, Shipfitter's Shop, Seventh Street near Avenue C, Adjacent to Repair Basins, Pearl City, Honolulu County, HI

  12. 26. DETAIL OF STRUCTURAL COLLAPSE OF TOP FLOOR OF MILL, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. DETAIL OF STRUCTURAL COLLAPSE OF TOP FLOOR OF MILL, ABOVE ORE BIN, LOOKING WEST FROM TOP OF STAIRWAY IN CA-290-25. THE PIPE AT CENTER WAS USED TO SPREAD CRUSHED ORE COMING FROM THE JAW CRUSHER EVENLY TO ALL AREA OF THE ORE BIN BELOW. - Skidoo Mine, Park Route 38 (Skidoo Road), Death Valley Junction, Inyo County, CA

  13. 6. Exterior view, showing structural details and instrumentation at the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Exterior view, showing structural details and instrumentation at the walk-in entry level (bottom) of Test Cell 6, Systems Integration Laboratory Building (T-28), looking southwest. - Air Force Plant PJKS, Systems Integration Laboratory, Systems Integration Laboratory Building, Waterton Canyon Road & Colorado Highway 121, Lakewood, Jefferson County, CO

  14. 10. Exterior view, showing the structural details and tanks above ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. Exterior view, showing the structural details and tanks above at walk-in entry level (bottom) of Test Cell 7, Systems Integration Laboratory Building (T-28), looking west. - Air Force Plant PJKS, Systems Integration Laboratory, Systems Integration Laboratory Building, Waterton Canyon Road & Colorado Highway 121, Lakewood, Jefferson County, CO

  15. Structure A, architectural sections & details. Drawing no. H2, revised ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Structure A, architectural sections & details. Drawing no. H2, revised as-built dated October 11, 1951. Original drawing by Black & Veatch, consulting engineers, Kansas City, Missouri, prepared for the U.S. Department of the Army, Office of Engineers, Military Construction Division, Washington, D.C. dated October 1. - Travis Air Force Base, Building No. 925, W Street, Fairfield, Solano County, CA

  16. Detail interior view of northeast stay tower at parking structure ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail interior view of northeast stay tower at parking structure in Section A showing graffiti, looking south between levels B3 and B4. Graffiti reads "God bless our local 3 brothers who gave their lives on 9-11-01 and all the rest! Amen" (BH) - World Trade Center Site, Bounded by Vesey, Church, Liberty Streets, & Route 9A, New York County, NY

  17. Detail Hframe structure about five and onefourth miles southwest of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail H-frame structure about five and one-fourth miles southwest of Morony Dam and Powerhouse showing one modern non-ceramic insulator and two historic porcelain suspension insulators - Morony Hydroelectric Facility, Morony-to-Rainbow 100 kV Transmission Line, West bank of the Missouri River, Great Falls, Cascade County, MT

  18. Detail of insulator array at first line structure showing historic ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of insulator array at first line structure showing historic porcelain suspension insulators in strings of eight, porcelain jumper support insulators in strings of six, arch rings and ball weights - Morony Hydroelectric Facility, Morony-to-Rainbow 100 kV Transmission Line, West bank of the Missouri River, Great Falls, Cascade County, MT

  19. 5. Interior Detail of Roof Structure and Trusses Note: Photographs ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Interior Detail of Roof Structure and Trusses Note: Photographs Nos. CA-1543F-6 through CA-1543F-19 are photocopies of construction drawings (various dates). Originals located at Mare Island Naval Shipyard-Staff Civil Engineer's Office. - Mare Island Naval Shipyard, Chemical Cleaning Facility, North of Fourteenth Street, between California & Railroad Avenue, Vallejo, Solano County, CA

  20. 35. DETAIL VIEW OF THE UNDERSIDE AND SUPPORT STRUCTURE OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    35. DETAIL VIEW OF THE UNDERSIDE AND SUPPORT STRUCTURE OF THE ORE BINS. VIEW WAS TAKEN FROM THE STAIR LANDING BETWEEN THE BREAKER LEVEL AND THE STAMP LEVEL. - Standard Gold Mill, East of Bodie Creek, Northeast of Bodie, Bodie, Mono County, CA

  1. 9. "TEST STAND; STRUCTURAL; CABLE TUNNEL, PLAN, SECTIONS, DETAILS." Specifications ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. "TEST STAND; STRUCTURAL; CABLE TUNNEL, PLAN, SECTIONS, DETAILS." Specifications No. OC1-55-72-(Rev.); Drawing No. 60-09-12; sheet 43 of 148; file no. AF 1320/94, Rev. A. Stamped: RECORD DRAWING - AS CONSTRUCTED. Below stamp: Contract no. 4338, no change. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Test Stand 1-A Terminal Room, Test Area 1-120, north end of Jupiter Boulevard, Boron, Kern County, CA

  2. 12. "TEST STAND; STRUCTURAL; DEFLECTOR PIT DETAILS, SHEET NO. 1." ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. "TEST STAND; STRUCTURAL; DEFLECTOR PIT DETAILS, SHEET NO. 1." Specifications No. ENG-04-353-55-72; Drawing No. 60-09-12; sheet 41 of 148; file no. 1320/92, Rev. A. Stamped: RECORD DRAWING - AS CONSTRUCTED. Below stamp: Contract no. 4338, no change. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Test Stand 1-A Terminal Room, Test Area 1-120, north end of Jupiter Boulevard, Boron, Kern County, CA

  3. 9. DETAIL OF DIVERSION STRUCTURE WEST OF DERBY LAKE (SECTION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. DETAIL OF DIVERSION STRUCTURE WEST OF DERBY LAKE (SECTION 2) SHOWING DIVERSION GATE TO LAKE LADORA. - Highline Canal, Sand Creek Lateral, Beginning at intersection of Peoria Street & Highline Canal in Arapahoe County (City of Aurora), Sand Creek lateral Extends 15 miles Northerly through Araphoe County, City & County of Denver, & Adams County to its end point, approximately 1/4 mile Southest of intersectioin of D Street & Ninth Avenue in Adams County (Rocky Mountain Arsenal, Commerce City Vicinity), Commerce City, Adams County, CO

  4. DETAIL VIEW, STRUCTURAL TIMBER AND FLOOR JOISTS, SOUTH GARRET. THIS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    DETAIL VIEW, STRUCTURAL TIMBER AND FLOOR JOISTS, SOUTH GARRET. THIS TIMBER IS ONE OF TWO EXTENDING OUT FROM THE HOUSE AND JOINED TO VERTICAL POSTS LOCATED WITHIN THE WOOD TUSCAN COLUMNS LOCATED AT THE PORTICO’S TWO OUTER CORNERS. THE TIMBERS AND THE VISIBLE FLOOR JOISTS WERE PART OF THE HOUSE’S INITIAL CA. 1770 CONSTRUCTION - The Woodlands, 4000 Woodlands Avenue, Philadelphia, Philadelphia County, PA

  5. 5. "TEST STAND 13, CONCRETE STRUCTURAL SECTIONS AND DETAILS." Specifications ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. "TEST STAND 1-3, CONCRETE STRUCTURAL SECTIONS AND DETAILS." Specifications No. OC12-50-10; Drawing No. 60-09-06; no sheet number within title block. D.O. SERIES 1109/17, Rev. A. Stamped: AS BUILT; NO CHANGES. Date of Revision A: 11/1/50. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Test Stand 1-3, Test Area 1-115, northwest end of Saturn Boulevard, Boron, Kern County, CA

  6. Detail View looking at the protected structure and landing gear ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail View looking at the protected structure and landing gear housing in the void created by the removal of the Forward Reaction Control System Module from the forward section of the Orbiter Discovery. This view was taken from the service platform in the Orbiter Processing Facility at Kennedy Space Center. - Space Transportation System, Orbiter Discovery (OV-103), Lyndon B. Johnson Space Center, 2101 NASA Parkway, Houston, Harris County, TX

  7. Aircraft wing structural detail design (wing, aileron, flaps, and subsystems)

    NASA Technical Reports Server (NTRS)

    Downs, Robert; Zable, Mike; Hughes, James; Heiser, Terry; Adrian, Kenneth

    1993-01-01

    The goal of this project was to design, in detail, the wing, flaps, and ailerons for a primary flight trainer. Integrated in this design are provisions for the fuel system, the electrical system, and the fuselage/cabin carry-through interface structure. This conceptual design displays the general arrangement of all major components in the wing structure, taking into consideration the requirements set forth by the appropriate sections of Federal Aviation Regulation Part 23 (FAR23) as well as those established in the statement of work.

  8. Ligand binding studies, preliminary structure-activity relationship and detailed mechanistic characterization of 1-phenyl-6,6-dimethyl-1,3,5-triazine-2,4-diamine derivatives as inhibitors of Escherichia coli dihydrofolate reductase

    PubMed Central

    Srinivasan, Bharath; Tonddast-Navaei, Sam; Skolnick, Jeffrey

    2015-01-01

    Gram-negative bacteria are implicated in the causation of life-threatening hospital-acquired infections. They acquire rapid resistance to multiple drugs and available antibiotics. Hence, there is the need to discover new antibacterial agents with novel scaffolds. For the first time, this study explores the 1,3,5-triazine-2,4-diamine and 1,2,4-triazine-2,4-diamine group of compounds as potential inhibitors of E. coli DHFR, a pivotal enzyme in the thymidine and purine synthesis pathway. Using differential scanning fluorimetry, DSF, fifteen compounds with various substitutions on either the 3rd or 4th positions on the benzene group of 6,6-dimethyl-1-(benzene)-1,3,5-triazine-2,4-diamine were shown to bind to the enzyme with varying affinities. Then, the dose dependence of inhibition by these compounds was determined. Preliminary quantitative structure-activity relationship analysis and docking studies implicate the alkyl linker group and the sulfonyl fluoride group in increasing the potency of inhibition. 4-[4-[3-(4,6-diamino-2,2-dimethyl-1,3,5-triazin-1-yl)phenyl]butyl]benzenesulfonyl fluoride (NSC120927), the best hit from the study and a molecule with no reported inhibition of E. coli DHFR, potently inhibits the enzyme with a Ki value of 42.50 ± 5.34 nM, followed by 4-[6-[4-(4,6-diamino-2,2-dimethyl-1,3,5-triazin-1-yl)phenyl]hexyl]benzenesulfonyl fluoride(NSC132279), with a Ki value of 100.9 ± 12.7 nM. Detailed kinetic characterization of the inhibition brought about by five small-molecule hits shows that these inhibitors bind to the dihydrofolate binding site with preferential binding to the NADPH-bound binary form of the enzyme. Furthermore, in search of novel diaminotriazine scaffolds, it is shown that lamotrigine, a 1,2,4-triazine-3,5-diamine and a sodium-ion channel blocker class of antiepileptic drug, also inhibits E. coli DHFR. This is the first comprehensive study on the binding and inhibition brought about by diaminotriazines of a gram

  9. Partially Assembled Nucleosome Structures at Atomic Detail.

    PubMed

    Rychkov, Georgy N; Ilatovskiy, Andrey V; Nazarov, Igor B; Shvetsov, Alexey V; Lebedev, Dmitry V; Konev, Alexander Y; Isaev-Ivanov, Vladimir V; Onufriev, Alexey V

    2017-02-07

    The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

  10. 115. Stage Level floor structure. Detail of the ends of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    115. Stage Level floor structure. Detail of the ends of three movable stage floor sections. An inclined steel angle track attached to the web of the floor beam allows the sections to roll under the fixed floor. The upper section of the inclined track is hinged so it can be moved upward by a cam mechanism to raise the end of the movable section level with the stage floor. A similar mechanism was used to open and close the floor sections for the star lifts (see sheet 4 of 9, note 6; sheet 8 of 9, details 5, 6A and 6B; sheet 6 of 9, notes 2A, 2B, and 3; and photo IL-1007-120). The pulley, and tongue extending out from the end of the movable section, were used to move the sections back and forth. - Auditorium Building, 430 South Michigan Avenue, Chicago, Cook County, IL

  11. Detailed electromagnetic simulation for the structural color of butterfly wings.

    PubMed

    Lee, R Todd; Smith, Glenn S

    2009-07-20

    Many species of butterflies exhibit interesting optical phenomena due to structural color. The physical reason for this color is subwavelength features on the surface of a single scale. The exposed surface of a scale is covered with a ridge structure. The fully three-dimensional, periodic, finite-difference time-domain method is used to create a detailed electromagnetic model of a generic ridge. A novel method for presenting the three-dimensional observed color pattern is developed. Using these tools, the change in color that is a result of varying individual features of the scale is explored. Computational models are developed that are similar to three butterflies: Morpho rhetenor, Troides magellanus, and Ancyluris meliboeus.

  12. Detailed temporal structure of communication networks in groups of songbirds

    PubMed Central

    Clayton, David

    2016-01-01

    Animals in groups often exchange calls, in patterns whose temporal structure may be influenced by contextual factors such as physical location and the social network structure of the group. We introduce a model-based analysis for temporal patterns of animal call timing, originally developed for networks of firing neurons. This has advantages over cross-correlation analysis in that it can correctly handle common-cause confounds and provides a generative model of call patterns with explicit parameters for the influences between individuals. It also has advantages over standard Markovian analysis in that it incorporates detailed temporal interactions which affect timing as well as sequencing of calls. Further, a fitted model can be used to generate novel synthetic call sequences. We apply the method to calls recorded from groups of domesticated zebra finch (Taeniopygia guttata) individuals. We find that the communication network in these groups has stable structure that persists from one day to the next, and that ‘kernels’ reflecting the temporal range of influence have a characteristic structure for a calling individual's effect on itself, its partner and on others in the group. We further find characteristic patterns of influences by call type as well as by individual. PMID:27335223

  13. Detailed temporal structure of communication networks in groups of songbirds.

    PubMed

    Stowell, Dan; Gill, Lisa; Clayton, David

    2016-06-01

    Animals in groups often exchange calls, in patterns whose temporal structure may be influenced by contextual factors such as physical location and the social network structure of the group. We introduce a model-based analysis for temporal patterns of animal call timing, originally developed for networks of firing neurons. This has advantages over cross-correlation analysis in that it can correctly handle common-cause confounds and provides a generative model of call patterns with explicit parameters for the influences between individuals. It also has advantages over standard Markovian analysis in that it incorporates detailed temporal interactions which affect timing as well as sequencing of calls. Further, a fitted model can be used to generate novel synthetic call sequences. We apply the method to calls recorded from groups of domesticated zebra finch (Taeniopygia guttata) individuals. We find that the communication network in these groups has stable structure that persists from one day to the next, and that 'kernels' reflecting the temporal range of influence have a characteristic structure for a calling individual's effect on itself, its partner and on others in the group. We further find characteristic patterns of influences by call type as well as by individual.

  14. Detailed analysis of structure and particle trajectories in sheared suspensions

    NASA Astrophysics Data System (ADS)

    Morris, Jeffrey; Katyal, Bhavana

    1999-11-01

    The structure and particle dynamics of sheared suspensions of hard spheres over a range of shear strength to Brownain motion (Péclet number, Pe) have been studied by detailed analysis of extended sampling of Stokesian Dynamics simulations of simple shear. The emphasis is upon large Pe. The structure has been analyzed by decomposition of the pair distribution function, g(r), into spherical harmonics; the harmonics are a complete set for the decompositon. The results indicate a profound and very marked change in structure due to shearing. It is shown that as Pe increases, the structure is increasingly distorted from teh equilibrium spherical symmetry and the number of harmonics required to recompose the original data to within an arbitrary accuracy increases, and this variation depends upon particle fraction. We present information on the content of the dominant harmonics as a function of radial distance for a pair, and interpret the results in terms of preferred directions in the material. Dynamic particle trajectories at time scales long relative to that used for the Brownian step are analyzed in a novel fashion by simple differential geometric measures, such as root mean square path curvature and torsion. Preliminary results illustrate that the path variation from mean flow correlates with the particle stress.

  15. Detailed characterization of the LLNL imaging proton spectrometer

    NASA Astrophysics Data System (ADS)

    Rasmus, A. M.; Hazi, A. U.; Manuel, M. J.-E.; Kuranz, C. C.; Klein, S. R.; Belancourt, P. X.; Fein, J. R.; MacDonald, M. J.; Drake, R. P.; Pollock, B. B.; Park, J.; Williams, G. J.; Chen, H.

    2016-11-01

    Ultra-intense short pulse lasers incident on solid targets (e.g., thin Au foils) produce well collimated, broad-spectrum proton beams. These proton beams can be used to characterize magnetic fields, electric fields, and density gradients in high energy-density systems. The LLNL-Imaging Proton Spectrometer (L-IPS) was designed and built [H. Chen et al., Rev. Sci. Instrum. 81, 10D314 (2010)] for use with such laser produced proton beams. The L-IPS has an energy range of 50 keV-40 MeV with a resolving power (E/dE) of about 275 at 1 MeV and 21 at 20 MeV, as well as a single spatial imaging axis. In order to better characterize the dispersion and imaging capability of this diagnostic, a 3D finite element analysis solver is used to calculate the magnetic field of the L-IPS. Particle trajectories are then obtained via numerical integration to determine the dispersion relation of the L-IPS in both energy and angular space.

  16. Detailed characterization of the LLNL imaging proton spectrometer

    SciTech Connect

    Rasmus, A. M.; Hazi, A. U.; Manuel, M. J. -E.; Kuranz, C. C.; Klein, S. R.; Belancourt, P. X.; Fein, J. R.; MacDonald, M. J.; Drake, R. P.; Pollock, B. B.; Park, J.; Williams, G. J.; Chen, H.

    2016-09-01

    Here, ultra-intense short pulse lasers incident on solid targets (e.g., several um thick Au foils) produce well collimated, broad-energy-spectrum proton beams. These proton beams can be used to characterize magnetic fields, electric fields (through particle deflection), and density gradients (through collisions) in high energy-density systems. The LLNL-Imaging Proton Spectrometer (L-IPS) was designed and built for use with such laser produced proton beams. The L-IPS has an energy range of 50 keV-40 MeV with a resolving power (E/dE) of about 275 at 1 MeV and 21 at 20 MeV, as well as a single spatial imaging axis. The protons enter the diagnostic through a vertical slit, aligned with a magnetic field imposed by permanent magnets. The protons are deflected perpendicular to the magnetic field (and therefor slit), so that spatial information in the direction of the slit is preserved. The extent to which the protons are bent by the magnetic field depends on the energy, so that the energy of the protons can be resolved as well. The protons are then measured by image plates, in which a meta-stable state is excited by collisions with the protons, which can later be imaged by a scanner. In order to better characterize the dispersion and imaging capability of this diagnostic, a 3D finite element analysis solver is used to calculate the magnetic field of the L-IPS. Particle trajectories are then obtained via numerical integration to determine the dispersion relation of the L-IPS in both energy and angular space.

  17. Detailed characterization of the LLNL imaging proton spectrometer

    DOE PAGES

    Rasmus, A. M.; Hazi, A. U.; Manuel, M. J. -E.; ...

    2016-09-01

    Here, ultra-intense short pulse lasers incident on solid targets (e.g., several um thick Au foils) produce well collimated, broad-energy-spectrum proton beams. These proton beams can be used to characterize magnetic fields, electric fields (through particle deflection), and density gradients (through collisions) in high energy-density systems. The LLNL-Imaging Proton Spectrometer (L-IPS) was designed and built for use with such laser produced proton beams. The L-IPS has an energy range of 50 keV-40 MeV with a resolving power (E/dE) of about 275 at 1 MeV and 21 at 20 MeV, as well as a single spatial imaging axis. The protons enter themore » diagnostic through a vertical slit, aligned with a magnetic field imposed by permanent magnets. The protons are deflected perpendicular to the magnetic field (and therefor slit), so that spatial information in the direction of the slit is preserved. The extent to which the protons are bent by the magnetic field depends on the energy, so that the energy of the protons can be resolved as well. The protons are then measured by image plates, in which a meta-stable state is excited by collisions with the protons, which can later be imaged by a scanner. In order to better characterize the dispersion and imaging capability of this diagnostic, a 3D finite element analysis solver is used to calculate the magnetic field of the L-IPS. Particle trajectories are then obtained via numerical integration to determine the dispersion relation of the L-IPS in both energy and angular space.« less

  18. Detailed temperature mapping-Warming characterizes archipelago zones

    NASA Astrophysics Data System (ADS)

    Veneranta, L.; Vanhatalo, J.; Urho, L.

    2016-12-01

    Rapidly warming shallow archipelago areas have the best energetic options for high ecological production. We analyzed and visualized the spring and summer temperature development in the Finnish coastal areas of the Northern Baltic Sea. Typical for the Baltic is a high annual periodicity and variability in water temperatures. The maximum difference between a single day average temperatures across the study area was 28.3 °C. During wintertime the littoral water temperature can decrease below zero in outer archipelago or open water areas when the protective ice cover is not present and the lowest observed value was -0.5 °C. The depth and exposition are the most important variables explaining the coastal temperature gradients from the innermost to the outermost areas in springtime when water is heated by increasing solar radiation. Temperature differs more within coastal area than between the basins. Water temperature sum was highest in innermost areas, lowest in open water areas and the variation in daily averages was highest in the middle region. At the end of the warming period, the difference in surface water temperatures between the innermost and outermost areas had diminished at the time when the cooling began in August-September. These clear temperature gradients enabled us use the cumulative water temperature to classify the coastal zones in a biologically sensible manner into five regions. Our study shows a novel approach to study detailed spatial variations in water temperatures. The results can further be used, for example, to model and predict the spatial distribution of aquatic biota and to determine appropriate spatio-temporal designs for aquatic biota surveys. The new spatial knowledge of temperature regions will also help the evaluation of possible causes of larger scale climatological changes in a biological context including productivity.

  19. Mineralogical characterization of rendering mortars from decorative details of a baroque building in Kozuchow (SW Poland)

    SciTech Connect

    Bartz, W.; Filar, T.

    2010-01-15

    Optical microscopic observations, scanning electron microscopy and microprobe with energy dispersive X-ray analysis, X-ray diffraction and differential thermal/thermogravimetric analysis allowed detailed characterization of rendering mortars from decorative details (figures of Saints) of a baroque building in Kozuchow (Lubuskie Voivodship, Western Poland). Two separate coats of rendering mortars have been distinguished, differing in composition of their filler. The under coat mortar has filler composed of coarse-grained siliceous sand, whereas the finishing one has much finer grained filler, dominated by a mixture of charcoal and Fe-smelting slag, with minor amounts of quartz grains. Both mortars have air-hardening binder composed of gypsum and micritic calcite, exhibiting microcrystalline structure.

  20. ELECTRON MICROSCOPY OF STRUCTURAL DETAIL IN FROZEN BIOLOGICAL SPECIMENS

    PubMed Central

    Steere, Russell L.

    1957-01-01

    A procedure is described whereby preshadowed replicas can be obtained from frozen biological specimens which have been cut and then etched by sublimation of the ice from their surfaces. Electron micrographs showing details of the internal structure of plant virus crystals are presented to demonstrate the values of the procedure. Crystals of purified tobacco ringspot virus and squash mosaic virus and some portions of turnip yellow mosaic virus crystals have been shown to exhibit hexagonal packing. Sections through in situ crystals of tobacco mosaic virus show the rods to be parallel within each layer and arranged in a square net as viewed end on. Individual rods in each layer of the latter measure 300 mµ in length and are somewhat tilted with respect to the rods of adjacent layers. This results in the formation of a herring-bone appearance when a crystal is cut perpendicular to its hexagonal face. It is suggested that the procedure outlined here might well serve to supplement other procedures for the preparation of many cytological specimens for electron microscopy. PMID:13416310

  1. Investigating structural details of lipid-cholesterol-A β interactions

    NASA Astrophysics Data System (ADS)

    Rai, Durgesh; Anunciado, Divina; Heller, William; O'Neill, Hugh; Urban, Volker; Qian, Shuo

    2015-03-01

    Alzheimer's disease (AD) is the most common form of dementia and is predicted to affect 1 in 85 people around the world by 2050. Amyloid beta (A β) -peptide, a peptide composed of 40- 42 amino acids that is the product of cleavage from the amyloid precursor protein (APP), is regarded to play a major role in the development of AD. In addition, accumulating evidence points to a positive association between cholesterol and AD. Here, we present results from our studies about A β-peptide and cholesterol in bilayer by small-angle neutron scattering (SANS) using a combination of dimyristoyl, phosphocholine (DMPC) and partially deuterated cholesterol (cholesterol-d7) with and without A β. We compare the results using grazing incidence and transmission SANS on lipid bilayer films and unilamellar vesicles respectively. The structural details on vesicles and bilayers work in conjunction with the circular dichroism on peptide in solution and oriented circular dichroism in bilayer films. The studies confirm a positive association of A β with the membrane layers. The results from different studies will be compared and contrasted in presentation.

  2. Detailed slab and mantle structure beneath westernmost Mediterranean

    NASA Astrophysics Data System (ADS)

    Sun, D.; Miller, M. S.; Bezada, M. J.; Humphreys, E.

    2013-12-01

    The geological evolution of the westernmost Mediterranean holds an important piece of the puzzle of how whole western Mediterranean evolved due to the convergence of Africa with Eurasia. Detailed upper mantle seismological images are crucial to test two controversial ideas about the dynamic process of the westernmost Mediterranean during the Cenozoic: slab rollback and lithosphere delamination. Recent tomographic images based on the dense seismic network in Spain and northern Morocco reveal a high-resolution continuous high-velocity anomaly to the transition zone depth under the Alboran domain [Bezada and Humphreys, 2013], which was used to support the slab roll back hypothesis for the westernmost Mediterranean tectonic evolution. However, the slab shape, width, and sharpness of its edges are not well resolved. Furthermore, the deep 2010 earthquake beneath Granada, Spain suggests possible oceanic crust material existing at ~ 600 km depth, which cannot be resolved by current tomography models. The study of multipathing and waveform broadening around sharp features has proven an efficient way to study those features. Here, we use both P and S waveform data from the PICASSO array to produce a detailed image. For the deep Granada earthquake, high frequency second arrivals and long coda after the P and S arrivals are shown on stations in the Rif Mountains of Morocco. By fitting both SH and P waveform data, we suggest that a low-velocity layer (LVL, 2 km thickness, δVs = -10%), possibly old oceanic crust, sits on top of the slab. The seismic waves travel through the LVL as guided waves preserving their high frequency energy. The strength of the second arrivals are very sensitive to the relative location between the deep earthquake and the LVL, which indicates the 2010 deep earthquake was most-likely within the subducted oceanic crust. Using both teleseismic and regional data, we conclude that the width of the sub-vertical slab is ~150 km, which is sharper than the

  3. Detailed characterization of lithium diffusion mechanisms in crystalline silicon using the kinetic Activation-Relaxation Technique

    NASA Astrophysics Data System (ADS)

    Trochet, Mickaël; Restrepo Gutierrez, Oscar Antonio; Mousseau, Normand

    Silicon displays a potential for high-capacity anode material for lithium-ion batteries as it can absorb large quantities of this metal. Yet, very little is understood about the evolution of diffusion mechanisms and migration barriers as the concentration of lithium increases. Until now, for example, simulations studies were limited by the time scale over which diffusion takes place. Here, we use the kinetic activation relaxation technique (kART), an unbiased off-lattice Monte Carlo method with on-the fly catalog building, coupled with the ReaxFF forcefield to follow diffusion of Li in c - Si over timescale of seconds and more at room temperature, obtaining detailed information about the whole set of possible diffusion mechanisms as the local environment evolves. We first present a detailed characterization of Li diffusion in the presence of 1 to 3 impurities and then show the evolution of systems with a higher concentration of solute as Li aggregate. These results provide a first detailed picture of the onset of Li aggregating into this high-capacity material, as it modifies the structure through local rearrangements and long-range elastic deformations, crucial information for the development of the next generation of high-capacity anode. ∖pard ∖pard.

  4. Structural characterization of solid foams

    NASA Astrophysics Data System (ADS)

    Maire, Éric; Adrien, Jérôme; Petit, Clémence

    2014-10-01

    For being a useful contribution to the understanding of the properties of solid foams, the characterization of the structure of solid foams has to be performed at different scales. The microstructure of the solid part of the foams has to be analyzed. For this, standard SEM observations are often used. The most important aspect (and the most problematic) remains the characterization of the porous architecture of these materials. The methods introduced in this paper concern both scales and the article discusses the specificity of the experiments in the case of porous materials. X-ray tomography is described in more details because it becomes widely used for this purpose. The paper also shows how the obtained 3D images (sometimes obtained during deformation) can be processed to yield important morphological parameters describing the foams. xml:lang="fr"

  5. A new laboratory-scale experimental facility for detailed aerothermal characterizations of volumetric absorbers

    NASA Astrophysics Data System (ADS)

    Gomez-Garcia, Fabrisio; Santiago, Sergio; Luque, Salvador; Romero, Manuel; Gonzalez-Aguilar, Jose

    2016-05-01

    This paper describes a new modular laboratory-scale experimental facility that was designed to conduct detailed aerothermal characterizations of volumetric absorbers for use in concentrating solar power plants. Absorbers are generally considered to be the element with the highest potential for efficiency gains in solar thermal energy systems. The configu-ration of volumetric absorbers enables concentrated solar radiation to penetrate deep into their solid structure, where it is progressively absorbed, prior to being transferred by convection to a working fluid flowing through the structure. Current design trends towards higher absorber outlet temperatures have led to the use of complex intricate geometries in novel ceramic and metallic elements to maximize the temperature deep inside the structure (thus reducing thermal emission losses at the front surface and increasing efficiency). Although numerical models simulate the conjugate heat transfer mechanisms along volumetric absorbers, they lack, in many cases, the accuracy that is required for precise aerothermal validations. The present work aims to aid this objective by the design, development, commissioning and operation of a new experimental facility which consists of a 7 kWe (1.2 kWth) high flux solar simulator, a radiation homogenizer, inlet and outlet collector modules and a working section that can accommodate volumetric absorbers up to 80 mm × 80 mm in cross-sectional area. Experimental measurements conducted in the facility include absorber solid temperature distributions along its depth, inlet and outlet air temperatures, air mass flow rate and pressure drop, incident radiative heat flux, and overall thermal efficiency. In addition, two windows allow for the direct visualization of the front and rear absorber surfaces, thus enabling full-coverage surface temperature measurements by thermal imaging cameras. This paper presents the results from the aerothermal characterization of a siliconized silicon

  6. Detailed requirements for a next generation nuclear data structure.

    SciTech Connect

    Brown, D.

    2016-07-05

    This document attempts to compile the requirements for the top-levels of a hierarchical arrangement of nuclear data such as found in the ENDF format. This set of requirements will be used to guide the development of a new data structure to replace the legacy ENDF format.

  7. Cutinisation of tomato fruit epidermis: Structural and morphological details

    PubMed Central

    Segado, Patricia; Domínguez, Eva; Heredia, Antonio

    2016-01-01

    ABSTRACT In tomato, the ovary is covered with a thin, electron-dense and uniform cuticle. The first 10 d after anthesis are critical in the cutinisation of the outer epidermal wall. During this period, singular cytoplasmic domains have been identified in the epidermal cells which seem to be involved in lipid biosynthesis. Moreover, the inner side of the procuticle showed a globular structure with vesicle-like particles of different size that seemed to migrate from the cytoplasm to the procuticle. These electron-dense particles are postulated to play an important role in early cutin synthesis. PMID:27031163

  8. Results of Detailed Hydrologic Characterization Tests—Fiscal and Calendar Year 2005

    SciTech Connect

    Spane, Frank A.; Newcomer, Darrell R.

    2008-02-27

    This report provides the results of detailed hydrologic characterization tests conducted within selected Hanford Site wells during fiscal and calendar year 2005. Detailed characterization tests performed included groundwater-flow characterization, barometric response evaluation, slug tests, in-well vertical groundwater-flow assessments, and a single-well tracer and constant-rate pumping test. Hydraulic property estimates obtained from the detailed hydrologic tests include hydraulic conductivity, transmissivity, specific yield, effective porosity, in-well lateral and vertical groundwater-flow velocity, aquifer groundwater-flow velocity, and depth-distribution profiles of hydraulic conductivity. In addition, local groundwater-flow characteristics (i.e., hydraulic gradient and flow direction) were determined for a site where detailed well testing was performed. Results obtained from these tests provide hydrologic information that supports the needs of Resource Conservation and Recovery Act waste management area characterization as well as sitewide groundwater monitoring and modeling programs. These results also reduce the uncertainty of groundwater-flow conditions at selected locations on the Hanford Site.

  9. Detailed structural characterization of the grafting of [Ta(=CHtBu)(CH2tBu)3] and [Cp*TaMe4] on silica partially dehydroxylated at 700 C and the activity of the grafted complexes toward alkane metathesis

    SciTech Connect

    Le Roux, Erwan; Chabanas, Mathieu; Baudouin, Anne; de Mallmann, Aimery; Coperet, Christophe; Quadrelli, E. Allesandra; Thivolle-Cazat, Jean; Basset, Jean-Marie; Lukens, Wayne; Lesage, Anne; Emsley, Lyndon; Sunley, Glenn J.

    2004-08-30

    The reaction of [Ta({double_bond}CHtBu)(CH{sub 2}tBu){sub 3}] or [Cp*Ta(CH{sub 3}){sub 4}] with a silica partially dehydroxylated at 700 C gives the corresponding monosiloxy surface complexes [({triple_bond}SiO)Ta({double_bond}CHtBu)(CH{sub 2}tBu){sub 2}] and [({triple_bond}SiO)Ta(CH{sub 3}){sub 3}Cp*] by eliminating a {sigma}-bonded ligand as the corresponding alkane (H-CH{sub 2}tBu or H-CH{sub 3}). EXAFS data show that an adjacent siloxane bridge of the surface plays the role of an extra surface ligand, which most likely stabilizes these complexes as in [({triple_bond}SiO)Ta({double_bond}CHtBu)(CH{sub 2}tBu){sub 2}({triple_bond}SiOSi{triple_bond})] (1a') and [({triple_bond}SiO)Ta(CH{sub 3}){sub 3}Cp*({triple_bond}SiOSi{triple_bond})] (2a'). In the case of [({triple_bond}SiO)Ta({double_bond}CHtBu)(CH{sub 2}tBu){sub 2}({triple_bond}SiOSi{triple_bond})], the structure is further stabilized by an additional interaction: a C-H agostic bond as evidenced by the small J coupling constant for the carbenic C-H (H{sub C-H} = 80 Hz), which was measured by J-resolved 2D solid-state NMR spectroscopy. The product selectivity in propane metathesis in the presence of [({triple_bond}SiO)Ta({double_bond}CHtBu)-(CH{sub 2}tBu){sub 2}({triple_bond}SiOSi{triple_bond})] (1a') as a catalyst precursor and the inactivity of the surface complex [({triple_bond}SiO)Ta-(CH{sub 3}){sub 3}Cp*({triple_bond}SiOSi{triple_bond})] (2a') show that the active site is required to be highly electrophilic and probably involves a metallacyclobutane intermediate.

  10. A Detailed Study on the Low-Energy Structures of Charged Colloidal Clusters.

    PubMed

    Cruz, S M A; Marques, J M C

    2016-04-07

    The target of this investigation is the systematic characterization of the low-energy structures of charged colloidal clusters that may be important to understand the self-assembling process of biomolecules. The aggregation of charged colloidal particles is governed by the attractive short-ranged Morse potential and the Yukawa repulsive tail to describe the long-range charge effect. A global optimization strategy, based on our own evolutionary algorithm, was adopted to discover the low-energy structures of colloidal clusters composed of up to 20 particles. A detailed analysis of the low-energy structures involving charged particles shows that the appearance of the Bernal spiral as the most stable motif occurs, first, at N = 6, but it is favored for larger clusters (N ≥ 13); for 6 ≤ N ≤ 12, there is a competition between the spiral (which is favored for higher charges) and more spherical-like structures. Finally, we study binary clusters composed by two sets of differently charged colloidal particles. Although a great diversity of low-energy structures is observed (especially for aggregates with one of the components in excess), the global minimum is disputed by three structural motifs depending on the composition of the cluster and, in some cases, on the range of the Morse potential.

  11. Content, Structure, and Sequence of the Detailing Discipline at Kendall College of Art and Design.

    ERIC Educational Resources Information Center

    Mulder, Bruce E.

    A study identified the appropriate general content, structure, and sequence for a detailing discipline that promoted student achievement to professional levels. Its focus was the detailing discipline, a sequence of studio courses within the furniture design program at Kendall College of Art and Design, Grand Rapids, Michigan. (Detailing, an…

  12. Detailed Geophysical Fault Characterization in Yucca Flat, Nevada Test Site, Nevada

    USGS Publications Warehouse

    Asch, Theodore H.; Sweetkind, Donald S.; Burton, Bethany L.; Wallin, Erin L.

    2009-01-01

    Yucca Flat is a topographic and structural basin in the northeastern part of the Nevada Test Site (NTS) in Nye County, Nevada. Between the years 1951 and 1992, 659 underground nuclear tests took place in Yucca Flat; most were conducted in large, vertical excavations that penetrated alluvium and the underlying Cenozoic volcanic rocks. Radioactive and other potential chemical contaminants at the NTS are the subject of a long-term program of investigation and remediation by the U.S. Department of Energy (DOE), National Nuclear Security Administration, Nevada Site Office, under its Environmental Restoration Program. As part of the program, the DOE seeks to assess the extent of contamination and to evaluate the potential risks to humans and the environment from byproducts of weapons testing. To accomplish this objective, the DOE Environmental Restoration Program is constructing and calibrating a ground-water flow model to predict hydrologic flow in Yucca Flat as part of an effort to quantify the subsurface hydrology of the Nevada Test Site. A necessary part of calibrating and evaluating a model of the flow system is an understanding of the location and characteristics of faults that may influence ground-water flow. In addition, knowledge of fault-zone architecture and physical properties is a fundamental component of the containment of the contamination from underground nuclear tests, should such testing ever resume at the Nevada Test Site. The goal of the present investigation is to develop a detailed understanding of the geometry and physical properties of fault zones in Yucca Flat. This study was designed to investigate faults in greater detail and to characterize fault geometry, the presence of fault splays, and the fault-zone width. Integrated geological and geophysical studies have been designed and implemented to work toward this goal. This report describes the geophysical surveys conducted near two drill holes in Yucca Flat, the data analyses performed, and the

  13. Detailed Geophysical Fault Characterization in Yucca Flat, Nevada Test Site, Nevada

    SciTech Connect

    Theodore H. Asch; Donald Sweetkind; Bethany L. Burton; Erin L. Wallin

    2009-02-10

    Yucca Flat is a topographic and structural basin in the northeastern part of the Nevada Test Site (NTS) in Nye County, Nevada. Between the years 1951 and 1992, 659 underground nuclear tests took place in Yucca Flat; most were conducted in large, vertical excavations that penetrated alluvium and the underlying Cenozoic volcanic rocks. Radioactive and other potential chemical contaminants at the NTS are the subject of a long-term program of investigation and remediation by the U.S. Department of Energy (DOE), National Nuclear Security Administration, Nevada Site Office, under its Environmental Restoration Program. As part of the program, the DOE seeks to assess the extent of contamination and to evaluate the potential risks to humans and the environment from byproducts of weapons testing. To accomplish this objective, the DOE Environmental Restoration Program is constructing and calibrating a ground-water flow model to predict hydrologic flow in Yucca Flat as part of an effort to quantify the subsurface hydrology of the Nevada Test Site. A necessary part of calibrating and evaluating a model of the flow system is an understanding of the location and characteristics of faults that may influence ground-water flow. In addition, knowledge of fault-zone architecture and physical properties is a fundamental component of the containment of the contamination from underground nuclear tests, should such testing ever resume at the Nevada Test Site. The goal of the present investigation is to develop a detailed understanding of the geometry and physical properties of fault zones in Yucca Flat. This study was designed to investigate faults in greater detail and to characterize fault geometry, the presence of fault splays, and the fault-zone width. Integrated geological and geophysical studies have been designed and implemented to work toward this goal. This report describes the geophysical surveys conducted near two drill holes in Yucca Flat, the data analyses performed, and the

  14. Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation

    NASA Astrophysics Data System (ADS)

    Köster, Stefan; van Pee, Katharina; Hudel, Martina; Leustik, Martin; Rhinow, Daniel; Kühlbrandt, Werner; Chakraborty, Trinad; Yildiz, Özkan

    2014-04-01

    Listeriolysin O (LLO) is an essential virulence factor of Listeria monocytogenes that causes listeriosis. Listeria monocytogenes owes its ability to live within cells to the pH- and temperature-dependent pore-forming activity of LLO, which is unique among cholesterol-dependent cytolysins. LLO enables the bacteria to cross the phagosomal membrane and is also involved in activation of cellular processes, including the modulation of gene expression or intracellular Ca2+ oscillations. Neither the pore-forming mechanism nor the mechanisms triggering the signalling processes in the host cell are known in detail. Here, we report the crystal structure of LLO, in which we identified regions important for oligomerization and pore formation. Mutants were characterized by determining their haemolytic and Ca2+ uptake activity. We analysed the pore formation of LLO and its variants on erythrocyte ghosts by electron microscopy and show that pore formation requires precise interface interactions during toxin oligomerization on the membrane.

  15. Probing the Detailed Seismic Velocity Structure of Subduction Zones Using Advanced Seismic Tomography Methods

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Thurber, C. H.

    2005-12-01

    Subduction zones are one of the most important components of the Earth's plate tectonic system. Knowing the detailed seismic velocity structure within and around subducting slabs is vital to understand the constitution of the slab, the cause of intermediate depth earthquakes inside the slab, the fluid distribution and recycling, and tremor occurrence [Hacker et al., 2001; Obara, 2002].Thanks to the ability of double-difference tomography [Zhang and Thurber, 2003] to resolve the fine-scale structure near the source region and the favorable seismicity distribution inside many subducting slabs, it is now possible to characterize the fine details of the velocity structure and earthquake locations inside the slab, as shown in the study of the Japan subduction zone [Zhang et al., 2004]. We further develop the double-difference tomography method in two aspects: the first improvement is to use an adaptive inversion mesh rather than a regular inversion grid and the second improvement is to determine a reliable Vp/Vs structure using various strategies rather than directly from Vp and Vs [see our abstract ``Strategies to solve for a better Vp/Vs model using P and S arrival time'' at Session T29]. The adaptive mesh seismic tomography method is based on tetrahedral diagrams and can automatically adjust the inversion mesh according to the ray distribution so that the inversion mesh nodes are denser where there are more rays and vice versa [Zhang and Thurber, 2005]. As a result, the number of inversion mesh nodes is greatly reduced compared to a regular inversion grid with comparable spatial resolution, and the tomographic system is more stable and better conditioned. This improvement is quite valuable for characterizing the fine structure of the subduction zone considering the highly uneven distribution of earthquakes within and around the subducting slab. The second improvement, to determine a reliable Vp/Vs model, lies in jointly inverting Vp, Vs, and Vp/Vs using P, S, and S

  16. Creating Imaginative Worlds: Unique Details and Structure in Norma Fox Mazer's Young Adult Fiction.

    ERIC Educational Resources Information Center

    Angel, Ann

    2001-01-01

    Discusses how writer Norma Fox Mazer has helped many readers make the leap between reality and imagination simply in the way she handles details in the lives of her characters. Explores the ideas of communicating with detail, experimenting with structure, and playing with time in crucial scenes. (SG)

  17. 36. ARCHITECTURAL AND STRUCTURAL DETAILS OF ELEVATOR HOUSING, NaK HEATER ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    36. ARCHITECTURAL AND STRUCTURAL DETAILS OF ELEVATOR HOUSING, NaK HEATER STACK ROOF FLASHING, HOOD ELEVATION DETAIL. INCLUDES PARTIAL 'BILL OF MATERIAL.' INEEL DRAWING NUMBER 200-0633-00-287-106361. FLUOR NUMBER 5775-CPP-633-A-11. - Idaho National Engineering Laboratory, Old Waste Calcining Facility, Scoville, Butte County, ID

  18. Detail of antenna tower structure, looking northnorthwest OvertheHorizon Backscatter ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of antenna tower structure, looking north-northwest - Over-the-Horizon Backscatter Radar Network, Tulelake Radar Site Receive Sector Five Antenna Array, Unnamed Road West of Double Head Road, Tulelake, Siskiyou County, CA

  19. 22. U.S. Route 60 grade separation structure. Detail of the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. U.S. Route 60 grade separation structure. Detail of the arch stones on the east elevation. View facing north. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  20. Comparison of different commercial FFDM units by means of physical characterization and contrast-detail analysis.

    PubMed

    Rivetti, Stefano; Lanconelli, Nico; Campanini, Renato; Bertolini, Marco; Borasi, Gianni; Nitrosi, Andrea; Danielli, Claudio; Angelini, Lidia; Maggi, Stefania

    2006-11-01

    The purpose of this study was to perform a complete evaluation of three pieces of clinical digital mammography equipment. Image quality was assessed by performing physical characterization and contrast-detail (CD) analysis. We considered three different FFDM systems: a computed radiography unit (Fuji "FCR 5000 MA") and two flat-panel units, the indirect conversion a-Si based GE "Senographe 2000D" and the direct conversion a-Si based IMS "Giotto Image MD." The physical characterization was estimated by measuring the MTF, NNPS, and DQE of the detectors with no antiscatter grid and over the clinical range of exposures. The CD analysis was performed using a CDMAM 3.4 phantom and custom software designed for automatic computation of the contrast-detail curves. The physical characterization of the three digital systems confirms the excellent MTF properties of the direct conversion flat-panel detector (FPD). We performed a relative standard deviation (RSD) analysis, for investigating the different components of the noise presented by the three systems. It turned out that the two FPDs show a significant additive component, whereas for the CR system the statistical noise is dominant. The multiplicative factor is a minor constituent for all the systems. The two FPDs demonstrate better DQE, with respect to the CR system, for exposures higher than 70 microGy. The CD analysis indicated that the three systems are not statistically different for detail objects with a diameter greater than 0.3 mm. However, the IMS system showed a statistically significant different response for details smaller than 0.3 mm. In this case, the poor response of the a-Se detector could be attributed to its high-frequency noise characteristics, since its MTF, NEQ, and DQE are not inferior to those of the other systems. The CD results were independent of exposure level, within the investigated clinical range. We observed slight variations in the CD results, due to the changes in the visualization

  1. Comparison of different computed radiography systems: Physical characterization and contrast detail analysis

    SciTech Connect

    Rivetti, Stefano; Lanconelli, Nico; Bertolini, Marco; Nitrosi, Andrea; Burani, Aldo; Acchiappati, Domenico

    2010-02-15

    Purpose: In this study, five different units based on three different technologies--traditional computed radiography (CR) units with granular phosphor and single-side reading, granular phosphor and dual-side reading, and columnar phosphor and line-scanning reading--are compared in terms of physical characterization and contrast detail analysis. Methods: The physical characterization of the five systems was obtained with the standard beam condition RQA5. Three of the units have been developed by FUJIFILM (FCR ST-VI, FCR ST-BD, and FCR Velocity U), one by Kodak (Direct View CR 975), and one by Agfa (DX-S). The quantitative comparison is based on the calculation of the modulation transfer function (MTF), noise power spectrum (NPS), and detective quantum efficiency (DQE). Noise investigation was also achieved by using a relative standard deviation analysis. Psychophysical characterization is assessed by performing a contrast detail analysis with an automatic reading of CDRAD images. Results: The most advanced units based on columnar phosphors provide MTF values in line or better than those from conventional CR systems. The greater thickness of the columnar phosphor improves the efficiency, allowing for enhanced noise properties. In fact, NPS values for standard CR systems are remarkably higher for all the investigated exposures and especially for frequencies up to 3.5 lp/mm. As a consequence, DQE values for the three units based on columnar phosphors and line-scanning reading, or granular phosphor and dual-side reading, are neatly better than those from conventional CR systems. Actually, DQE values of about 40% are easily achievable for all the investigated exposures. Conclusions: This study suggests that systems based on the dual-side reading or line-scanning reading with columnar phosphors provide a remarkable improvement when compared to conventional CR units and yield results in line with those obtained from most digital detectors for radiography.

  2. Detailed Characterization and Profiles of Crankcase and Diesel Particular Matter Exhaust Emissions Using Speciated Organics

    PubMed Central

    Zielinska, Barbara; Campbell, David; Lawson, Douglas R.; Ireson, Robert G.; Weaver, Christopher S.; Hesterberg, Thomas W.; Larson, Timothy; Davey, Mark; Liu, L.-J. Sally

    2008-01-01

    A monitoring campaign was conducted in August-September 2005 to compare different experimental approaches quantifying school bus self-pollution. As part of this monitoring campaign, a detailed characterization of PM2.5 diesel engine emissions from the tailpipe and crankcase emissions from the road draft tubes was performed. To distinguish between tailpipe and crankcase vent emissions, a deuterated alkane, n-hexatriacontane-d74 (n-C36D74) was added to the engine oil to serve as intentional quantitative tracers for lubricating oil PM emissions. This paper focuses on the detailed chemical speciation of crankcase and tailpipe PM emissions from two school buses used in this study. We found that organic carbon emission rates were generally higher from the crankcase than from the tailpipe for these two school buses, while elemental carbon contributed significantly only in the tailpipe emissions. The n-C36D74 that was added to the engine oil was emitted at higher rates from the crankcase than the tailpipe. Tracers of engine oil (hopanes, and steranes) were present in much higher proportion in crankcase emissions. Particle-associated PAH emission rates were generally very low (< 1 μg/km), but more PAH species were present in crankcase than in tailpipe emissions. The speciation of samples collected in the bus cabins was consistent with most of the bus self-pollution originating from crankcase emissions. PMID:18754490

  3. Detailed characterization and profiles of crankcase and diesel particulate matter exhaust emissions using speciated organics.

    PubMed

    Zielinska, Barbara; Campbell, David; Lawson, Douglas R; Ireson, Robert G; Weaver, Christopher S; Hesterberg, Thomas W; Larson, Timothy; Davey, Mark; Liu, L J Sally

    2008-08-01

    A monitoring campaign was conducted in August-September 2005 to compare different experimental approaches quantifying school bus self-pollution. As part of this monitoring campaign, a detailed characterization of PM2.5 diesel engine emissions from the tailpipe and crankcase emissions from the road draft tubes was performed. To distinguish between tailpipe and crankcase vent emissions, a deuterated alkane, n-hexatriacontane-d74 (n-C36D74) was added to the engine oil to serve as an intentional quantitative tracer for lubricating oil PM emissions. This paper focuses on the detailed chemical speciation of crankcase and tailpipe PM emissions from two school buses used in this study. We found that organic carbon emission rates were generally higher from the crankcase than from the tailpipe for these two school buses, while elemental carbon contributed significantly only in the tailpipe emissions. The n-C36D74 that was added to the engine oil was emitted at higher rates from the crankcase than the tailpipe. Tracers of engine oil (hopanes and steranes) were present in much higher proportion in crankcase emissions. Particle-associated PAH emission rates were generally very low (< 1 microg/km), but more PAH species were present in crankcase than in tailpipe emissions. The speciation of samples collected in the bus cabins was consistent with most of the bus self-pollution originating from crankcase emissions.

  4. Structural Characterization of Schladitz Whiskers.

    DTIC Science & Technology

    1982-05-01

    and Eicke, 9 ,14 Lashmore ,16 and Newkirk and Wilsdorf. 1 7 7 I The ultimate tensile strength (UTS) of polycrystalline steel whiskers has been reported...have * Private communication by D. S. Lashmore , L. J. Swartzendruber and L. H. Bennett. 17 a combined with Fe to Fe 3 C. It was calculated that 18 + 2...by Lashmore (1977), and Schladitz (1968) reported values approach- ing 8 GPa. The structural details described in the previous chapter do not fit into

  5. Detailed Studies on the Structure and Dynamics of Reacting Dusty Flows at Normal and Microgravity

    NASA Technical Reports Server (NTRS)

    Andac, M. Gurhan; Cracchiola, Brad; Egolfopoulos, Fokion N.; Campbell, Charles S.

    1999-01-01

    Dusty reacting flows are of particular interest for a wide range of applications. Inert particles can alter the flammability and extinction limits of a combustible mixture. Reacting particles can release substantial amount of heat and can be used either for power generation or propulsion. Accumulation of combustible particles in air can result in explosions which, for example, can occur in grain elevators, during lumber milling and in mine galleries. Furthermore, inert particles are used as flow velocity markers in reacting flows, and their velocity is measured by non-intrusive laser diagnostic techniques. Despite their importance, dusty reacting flows have been less studied and understood compared to gas phase as well as sprays. The addition of solid particles in a flowing gas stream can lead to strong couplings between the two phases, which can be of dynamic, thermal, and chemical nature. The dynamic coupling between the two phases is caused by the inertia that causes the phases to move with different velocities. Furthermore, gravitational, thermophoretic, photophoretic, electrophoretic, diffusiophoretic, centrifugal, and magnetic forces can be exerted on the particles. In general, magnetic, electrophoretic, centrifugal, photophoretic, and diffusiophoretic can be neglected. On the other hand, thermophoretic forces, caused by steep temperature gradients, can be important. The gravitational forces are almost always present and can affect the dynamic response of large particles. Understanding and quantifying the chemical coupling between two phases is a challenging task. However, all reacting particles begin this process as inert particles, and they must be heated before they participate in the combustion process. Thus, one must first understand the interactions of inert particles in a combustion environment. The in-detail understanding of the dynamics and structure of dusty flows can be only advanced by considering simple flow geometries such as the opposed

  6. Detailed Characterization of Particulates Emitted by Pre-Commercial Single-Cylinder Gasoline Compression Ignition Engine

    SciTech Connect

    Zelenyuk, Alla; Reitz, Paul; Stewart, Mark L.; Imre, D.; Loeper, Paul; Adams, Cory; Andrie, Michael; Rothamer, David; Foster, David E.; Narayanaswamy, Kushal; Najt, Paul M.; Solomon, Arun S.

    2014-08-01

    Gasoline Compression Ignition (GCI) engines have the potential to achieve high fuel efficiency and to significantly reduce both NOx and particulate matter (PM) emissions by operating under dilute partially-premixed conditions. This low temperature combustion strategy is dependent upon direct-injection of gasoline during the compression stroke and potentially near top dead center (TDC). The timing and duration of the in-cylinder injections can be tailored based on speed and load to create optimized conditions that result in a stable combustion. We present the results of advanced aerosol analysis methods that have been used for detailed real-time characterization of PM emitted from a single-cylinder GCI engine operated at different speed, load, timing, and number and duration of near-TDC fuel injections. PM characterization included 28 measurements of size and composition of individual particles sampled directly from the exhaust and after mass and/or mobility classification. We use these data to calculate particle effective density, fractal dimension, dynamic shape factors in free-molecular and transition flow regimes, average diameter of primary spherules, number of spherules, and void fraction of soot agglomerates.

  7. A detailed characterization of the adult mouse model of glycogen storage disease Ia.

    PubMed

    Salganik, Susan V; Weinstein, David A; Shupe, Thomas D; Salganik, Max; Pintilie, Dana G; Petersen, Bryon E

    2009-09-01

    Glycogen storage disease type Ia (GSDIa) is caused by a genetic defect in the hepatic enzyme glucose-6-phosphatase (G6Pase-alpha), which manifests as life-threatening hypoglycemia with related metabolic complications. A G6Pase-alpha knockout (KO) mouse model was generated to study potential therapies for correcting this disorder. Since then, gene therapy studies have produced promising results, showing long-term improvement in liver histology and glycogen metabolism. Under existing protocols, however, untreated KO pups seldom survived weaning. Here, we present a thorough characterization of the G6Pase-alpha KO mouse, as well as the husbandry protocol for rearing this strain to adulthood. These mice were raised with only palliative care, and characterized from birth through 6 months of age. Once KO mice have survived the very frail weaning period, their size, agility, serum lipids and glycemic control improve dramatically, reaching levels approaching their wild-type littermates. In addition, our data reveal that adult mice lacking G6Pase-alpha are able to mate and produce viable offspring. However, liver histology and glycogen accumulation do not improve with age. Overall, the reliable production of mature KO mice could provide a critical tool for advancing the GSDIa field, as the availability of a robust enzyme-deficient adult offers a new spectrum of treatment avenues that would not be tolerated by the frail pups. Most importantly, our detailed characterization of the adult KO mouse provides a crucial baseline for accurately gauging the efficacy of experimental therapies in this important model.

  8. AN ASSESSMENT OF SIMPLIFIED VS. DETAILED METHODOLOGIES FOR SSI ANALYSES OF DEEPLY EMBEDDED STRUCTURES.

    SciTech Connect

    XU,J.MILLER,C.HOFMAYER,C.GRAVES,H.

    2004-03-04

    Sponsored by the US Nuclear Regulatory Commission (NRC), Brookhaven National Laboratory (BNL) is carrying out a research program to develop a technical basis to support the safety evaluation of deeply embedded and/or buried (DEB) structures as proposed for advanced reactor designs. In this program, the methods and computer programs established for the assessment of soil-structure interaction (SSI) effects for the current generation of light water reactors are evaluated to determine their applicability and adequacy in capturing the seismic behavior of DEB structures. This paper presents an assessment of the simplified vs. detailed methodologies for seismic analyses of DEB structures. In this assessment, a lump-mass beam model is used for the simplified approach and a finite element representation is employed for the detailed method. A typical containment structure embedded in a soil profile representative of a typical nuclear power plant site was utilized, considering various embedment depths from shallow to full burial. BNL used the CARES program for the simplified model and the SASSI2000 program for the detailed analyses. The calculated response spectra at the key locations of the DEB structure are used for the performance assessment of the applied methods for different depths of burial. Included in the paper are: (1) the description of both the simplified and detailed models for the SSI analyses of the DEB structure, (2) the comparison of the analysis results for the different depths of burial between the two methods, and (3) the performance assessment of the analysis methodologies for SSI analyses of DEB structures. The resulting assessment from this study has indicated that simplified methods may be capable of capturing the seismic response for much deeper embedded structures than would be normally allowed by the standard practice.

  9. Detailed molecular characterization of castor oil ethoxylates by liquid chromatography multistage mass spectrometry.

    PubMed

    Nasioudis, Andreas; van Velde, Jan W; Heeren, Ron M A; van den Brink, Oscar F

    2011-10-07

    The molecular characterization of castor oil ethoxylates (CASEOs) was studied by reverse-phase liquid chromatography (RPLC) mass spectrometry (MS) and multistage mass spectrometry (MS(n)). The developed RPLC method allowed the separation of the various CASEO components, and especially, the baseline separation of multiple nominal isobars (same nominal mass) and isomers (same exact mass). MS and MS(n) were used for the determination and structure elucidation of various structures and for the discrimination of the isobars and isomers. Different ionization techniques and adduct ions were also tested for optimization of the MS detection and the MS(n) fragmentation. A unique fragmentation pathway of ricinoleic acid is proposed, which can be used as a marker of the polymerization process and the topology of ethoxylation in the CASEO. In addition, characteristic neutral losses of ricinoleic acid reveal its (terminal or internal) position in the molecule.

  10. Structure A, reinforcing details. Drawing No. H2302, as built, Original ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Structure A, reinforcing details. Drawing No. H2-302, as built, Original drawing by Black & Veatch, Consulting Engineers, Kansas City, Missouri, prepared for the U.S. Department of the Army, Office of Engineers, Military Construction Division, Washington, D.C. dated October 1, 1951. - Travis Air Force Base, Building No. 925, W Street, Fairfield, Solano County, CA

  11. Detail of insulator array at Hframe structure on RyantoRainbow Line ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of insulator array at H-frame structure on Ryan-to-Rainbow Line 1 about three miles southwest of Ryan Dam. Array has one historic porcelain suspension insulator and two non-ceramic insulators - Ryan Hydroelectric Facility, Ryan-to-Rainbow 100 kV Transmission Line, West bank of Missouri River, northeast of Great Falls, Great Falls, Cascade County, MT

  12. Detail of insulator array at Hframe structure on RyantoRainbow Line ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of insulator array at H-frame structure on Ryan-to-Rainbow Line 2 about three and one-fourth miles southwest of Ryan Dam. Array has three historic porcelain suspension insulators - Ryan Hydroelectric Facility, Ryan-to-Rainbow 100 kV Transmission Line, West bank of Missouri River, northeast of Great Falls, Great Falls, Cascade County, MT

  13. Detail of MoronytoRainbow Hframe structure just east of Ryan Dam ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of Morony-to-Rainbow H-frame structure just east of Ryan Dam Road showing three historic porcelain suspension insulators in strings of six. View to east - Morony Hydroelectric Facility, Morony-to-Rainbow 100 kV Transmission Line, West bank of the Missouri River, Great Falls, Cascade County, MT

  14. PLUG STORAGE BUILDING, TRA611. STRUCTURAL DETAILS. FACE PLATE. FOURTEEN OPENINGS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    PLUG STORAGE BUILDING, TRA-611. STRUCTURAL DETAILS. FACE PLATE. FOURTEEN OPENINGS LABELED FOR PLUGS FROM SPECIFIC SIZE GROUPS IN THE MTR. BLAW-KNOX 3150-811-2, 1/1951. INL INDEX NO. 531-0611-00-098-100694, REV. 1. - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

  15. STRUCTURAL DETAILS AND SECTIONS OF MAIN PROCESSING BUILDING (CPP601). INL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    STRUCTURAL DETAILS AND SECTIONS OF MAIN PROCESSING BUILDING (CPP-601). INL DRAWING NUMBER 200-0601-00-291-103079. ALTERNATE ID NUMBER 542-11-B-73. - Idaho National Engineering Laboratory, Idaho Chemical Processing Plant, Fuel Reprocessing Complex, Scoville, Butte County, ID

  16. Detailed imaging of flowing structures at depth using microseismicity: a tool for site investigation?

    NASA Astrophysics Data System (ADS)

    Pytharouli, S.; Lunn, R. J.; Shipton, Z. K.

    2011-12-01

    Field evidence shows that faults and fractures can act as focused pathways or barriers for fluid migration. This is an important property for modern engineering problems, e.g., CO2 sequestration, geological radioactive waste disposal, geothermal energy exploitation, land reclamation and remediation. For such applications the detailed characterization of the location, orientation and hydraulic properties of existing fractures is necessary. These investigations are expensive, requiring the hire of expensive equipment (excavator or drill rigs), which incur standing charges when not in use. In addition, they only provide information for discrete sample 'windows'. Non-intrusive methods have the ability to gather information across an entire area. Methods including electrical resistivity/conductivity and ground penetrating radar (GRP), have been used as tools for site investigations. Their imaging ability is often restricted due to unfavourable on-site conditions e.g. GRP is not useful in cases where a layer of clay or reinforced concrete is present. Our research has shown that high quality seismic data can be successfully used in the detailed imaging of sub-surface structures at depth; using induced microseismicity data recorded beneath the Açu reservoir in Brazil we identified orientations and values of average permeability of open shear fractures at depths up to 2.5km. Could microseismicity also provide information on the fracture width in terms of stress drops? First results from numerical simulations showed that higher stress drop values correspond to narrower fractures. These results were consistent with geological field observations. This study highlights the great potential of using microseismicity data as a supplementary tool for site investigation. Individual large-scale shear fractures in large rock volumes cannot currently be identified by any other geophysical dataset. The resolution of the method is restricted by the detection threshold of the local

  17. Characterizing atherosclerotic plaque with computed tomography: a contrast-detail study

    NASA Astrophysics Data System (ADS)

    Kasraie, Nima; Clarke, Geoffrey D.

    2012-02-01

    Plaque characterization may benefit from the increasing distinctiveness of the attenuating properties of different soft plaque components at lower energies. Due to the relative slight increase in the CT number of the nonadipose soft plaque at lower tube voltage settings vs. adipose plaque, a higher contrast between atheromous adipose and non-adipose plaque may become visible with modern 64 slice systems. A contrast-detail (C-D) phantom with varying plaque composition as the contrast generating method, was imaged on a commercial 64 slice MDCT system using 80, 120, and 140 kVp settings. The same phantom was also imaged on a Cone Beam CT (CBCT) system with a lower tube voltage of 75 kVp. The results of experiments from four different observers on three different plaque types (lipid, fiber, calcific) indicate that CT attenuation within lipid cores and fibrous masses vary not only with the percentage of lipid or fiber present, but also with the size of the cores. Furthermore, the C-D curve analysis for all three plaque types reveals that while the noise constraints prevent visible differentiation of soft plaque at current conventional 64 slice MDCT settings, CBCT exhibits superior visible contrast detectability than its conventional counterpart, with the latter having appreciably better resolution limits and beneficial lower tube voltages. This low voltage CT technique has the potential to be useful in composition based diagnosis of carotid vulnerable atherosclerotic plaque.

  18. Application of an ESI-QTOF method for the detailed characterization of GSK-3β inhibitors.

    PubMed

    De Simone, Angela; Fiori, Jessica; Naldi, Marina; D'Urzo, Annalisa; Tumiatti, Vincenzo; Milelli, Andrea; Andrisano, Vincenza

    2017-02-27

    The crucial role of Glycogen Synthase Kinase 3 (GSK-3β) as a pivotal player in Alzheimer's Disease (AD) has recently inspired significant attempts to design and synthesize potent kinase inhibitors. In fact GSK-3β is considered the main kinase which catalyzes the microtubule-associated protein tau hyper-phosphorylation and the neurofibrillary tangles (NFT) in vitro and in vivo, The first classes of GSK-3β inhibitors were classified as ATP-competitive and, therefore, they lack of an efficient degree of selectivity over other kinases. In light of this consideration, many efforts are devoted to characterize new non ATP-competitive GSK-3β inhibitors, endowed with high selectivity. In parallel, there is an urgent need to develop new analytical methodologies for the hit selection (highthroughput screening) and ligand binding characterization in terms of potency, affinity and mechanism of action. The new methodology for GSK-3β enzymatic activity determination can be adopted as a realistic alternative to the currently used radioactive, luminescence and fluorescence detection methods, each showing limitations in terms of safety and interferences. Herein, we propose an alternative and selective electrospray ionization quadrupole time-of-flight (ESI-QTOF) method, based on the direct quantification of phosphorylated substrate muscle glycogen synthase GSM, a peptide resembling the high affinity sequence of natural substrate muscle glycogen synthase 1, for the detailed characterization of GSK-3β inhibitors. The method was validated in terms of accuracy and reproducibility of GSM signal intensity with a relative standard deviation RSD% value of 3.55%; Limit of Detection (LOD): 0.006μM; Lower Limit of Quantification (LLOQ): 0.02μM; linearity r(2) 0.9951. The kinetic constants (KM and vmax) of the GSK-3β catalyzed kinase reaction and the inhibitory potency of known ligands (IC50), were determined. All the obtained results were in agreement with those reported in literature

  19. PROCESS WATER BUILDING, TRA605. BASEMENT FLOOR PLAN AND STRUCTURAL DETAILS. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    PROCESS WATER BUILDING, TRA-605. BASEMENT FLOOR PLAN AND STRUCTURAL DETAILS. SUMP TANK (DIAMETER 33 FEET; CAPACITY 100,000 GALLONS) LOCATION IN HIGH ROOF SECTION ON WEST SIDE. REPAIR SHOP AND STORAGE AREA IN LOW-ROOF AREA. WALL DETAILS: THICKNESS OF REINFORCED CONCRETE RANGES FROM 1'-6" TO 2' THICK. FOUNDATIONS FOR FIVE CELLS ENCLOSING PUMPS. BLAW-KNOX 3150-805-2, 12/1950. INL INDEX NO. 531-0605-62-098-100658, REV. 3. - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

  20. Detailed requirements document for the integrated structural analysis system, phase B

    NASA Technical Reports Server (NTRS)

    Rainey, J. A.

    1976-01-01

    The requirements are defined for a software system entitled integrated Structural Analysis System (ISAS) Phase B which is being developed to provide the user with a tool by which a complete and detailed analysis of a complex structural system can be performed. This software system will allow for automated interface with numerous structural analysis batch programs and for user interaction in the creation, selection, and validation of data. This system will include modifications to the 4 functions developed for ISAS, and the development of 25 new functions. The new functions are described.

  1. Detailed hydrodynamic characterization of harmonically excited falling-film flows: A combined experimental and computational study

    NASA Astrophysics Data System (ADS)

    Charogiannis, Alexandros; Denner, Fabian; van Wachem, Berend G. M.; Kalliadasis, Serafim; Markides, Christos N.

    2017-01-01

    We present results from the simultaneous application of planar laser-induced fluorescence (PLIF), particle image velocimetry (PIV) and particle tracking velocimetry (PTV), complemented by direct numerical simulations, aimed at the detailed hydrodynamic characterization of harmonically excited liquid-film flows falling under the action of gravity. The experimental campaign comprises four different aqueous-glycerol solutions corresponding to four Kapitza numbers (Ka=14 , 85, 350, 1800), spanning the Reynolds number range Re=2.3 -320 , and with forcing frequencies fw=7 and 10 Hz . PLIF was employed to generate spatiotemporally resolved film-height measurements, and PIV and PTV to generate two-dimensional velocity-vector maps of the flow field underneath the wavy film interface. The latter allows for instantaneous, highly localized velocity-profile, bulk-velocity, and flow-rate data to be retrieved, based on which the effect of local film topology on the flow field underneath the waves is studied in detail. Temporal sequences of instantaneous and local film height and bulk velocity are generated and combined into bulk flow-rate time series. The time-mean flow rates are then decomposed into steady and unsteady components, the former represented by the product of the mean film height and mean bulk velocity and the latter by the covariance of the film-height and bulk-velocity fluctuations. The steady terms are found to vary linearly with the flow Re, with the best-fit gradients approximated closely by the kinematic viscosities of the three examined liquids. The unsteady terms, typically amounting to 5 %-10 % of the mean and peaking at approximately 20 % , are found to scale linearly with the film-height variance. And, interestingly, the instantaneous flow rate is found to vary linearly with the instantaneous film height. Both experimental and numerical flow-rate data are closely approximated by a simple analytical relationship with only minor deviations. This relationship

  2. 12. "OBSERVATION POSTS, STRUCTURAL PLANS AND DETAILS." Specifications No. OC25572; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. "OBSERVATION POSTS, STRUCTURAL PLANS AND DETAILS." Specifications No. OC2-55-72; Drawing No. 60-09-12; sheet 89 of 148; file no. 1321/40, Rev. A. Very faint stamp above note reads: RECORD DRAWING - AS CONSTRUCTED. Below stamp: Contract no. 4338, no change. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Observation Bunkers for Test Stand 1-A, Test Area 1-120, north end of Jupiter Boulevard, Boron, Kern County, CA

  3. Structure A, protective alarm installation details. Drawing no. H3709, revised ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Structure A, protective alarm installation details. Drawing no. H3-709, revised as-built dated August 28, 1952. Original drawing by Black & Veatch, consulting engineers, Kansas City, Missouri, prepared for the U.S. Department of the Army, Office of Engineers, Military Construction Division, Washington, D.C. dated October 1, 1951. - Travis Air Force Base, Building No. 925, W Street, Fairfield, Solano County, CA

  4. PROCESS WATER BUILDING, TRA605. FIRST FLOOR PLAN WITH STRUCTURAL DETAILS. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    PROCESS WATER BUILDING, TRA-605. FIRST FLOOR PLAN WITH STRUCTURAL DETAILS. FLOOR SLABS AND HATCHES. SHOWER/LOCKER ROOM. STAIRWAYS. TWENTY-INCH-THICK WALL DIVIDES SUMP AND SEAL TANK CHAMBERS FROM REST OF FLOOR. BLAW-KNOX 3150-805-3, 1/1951. INL INDEX NO. 531-0605-62-098-100659, REV. 1. - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

  5. A&M. TAN607. Construction detail showing structural steel framework with reinforcing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    A&M. TAN-607. Construction detail showing structural steel framework with reinforcing steel in place prior to pouring concrete for biparting doors between hot shop and special equipment service (SES) room. Facing north. Hot shop to left, SES room to right. slot for north half of door shows at upper left of view. Date: May 21, 1954. INEEL negative no. 10548 - Idaho National Engineering Laboratory, Test Area North, Scoville, Butte County, ID

  6. Ultrasonic characterization of structural ceramics

    NASA Technical Reports Server (NTRS)

    Klima, S. J.; Baaklini, G. Y.

    1986-01-01

    Ultrasonic velocity and attenuation measurements were used to characterize density and microstructure in monolithic silicon nitride and silicon carbide. Research samples of these structural ceramics exhibited a wide range of density and microstructural variations. It was shown that bulk density variations correlate with and can be estimated by velocity measurements. Variations in microstructural features such as grain size or shape and pore morphology had a minor effect on velocity. However, these features had a pronounced effect on ultrasonic attenuation. The ultrasonic results are supplemented by low-energy radiography and scanning laser acoustic microscopy.

  7. Instrumentation for the Characterization of Inflatable Structures

    NASA Technical Reports Server (NTRS)

    Swanson, Gregory T.; Cassell, Alan M.; Johnson, R. Keith

    2012-01-01

    Current entry, descent, and landing technologies are not practical for heavy payloads due to mass and volume constraints dictated by limitations imposed by launch vehicle fairings. Therefore, new technologies are now being explored to provide a mass- and volume-efficient solution for heavy payload capabilities, including Inflatable Aerodynamic Decelerators (IAD) [1]. Consideration of IADs for space applications has prompted the development of instrumentation systems for integration with flexible structures to characterize system response to flight-like environment testing. This development opportunity faces many challenges specific to inflatable structures in extreme environments, including but not limited to physical flexibility, packaging, temperature, structural integration and data acquisition [2]. In the spring of 2012, two large scale Hypersonic Inflatable Aerodynamic Decelerators (HIAD) will be tested in the National Full-Scale Aerodynamics Complex s 40 by 80 wind tunnel at NASA Ames Research Center. The test series will characterize the performance of a 3.0 m and 6.0 m HIAD at various angles of attack and levels of inflation during flight-like loading. To analyze the performance of these inflatable test articles as they undergo aerodynamic loading, many instrumentation systems have been researched and developed. These systems will utilize new experimental sensing systems developed by the HIAD ground test campaign instrumentation team, in addition to traditional wind tunnel sensing techniques in an effort to improve test article characterization and model validation. During the 2012 test series the instrumentation systems will target inflatable aeroshell static and dynamic deformation, structural strap loading, surface pressure distribution, localized skin deflection, and torus inflation pressure. This paper will offer an overview of inflatable structure instrumentation, and provide detail into the design and implementation of the sensors systems that will

  8. Seismic retroftting of RC columns with RC jackets and wing walls with different structural details

    NASA Astrophysics Data System (ADS)

    Chang, Shuenn-Yih; Chen, Ting-Wei; Tran, Ngoc-Cuong; Liao, Wen-I.

    2014-06-01

    An original reinforced concrete (RC) column and four strengthened specimens, two with RC jackets and two with wing walls, were tested in this study. The original column specimen was designed to comply with older (pre-1999) design standards so that the usual detailing deficiencies in existing school buildings in Taiwan could be simulated. Two different structural details were chosen to fabricate the full-scale specimens for each retrofitting technique. The study confirmed that either RC jacketing or the installation of wing walls with two different structural details can effectively improve the stiffness and strength of an existing column. RC jacketing shows a better improvement in energy dissipation and ductility when compared to the columns with wing walls installed. This is because the two RC jacketed columns experienced a flexural failure, while a shear failure was found in the two columns with the wing walls installed, and thus led to a drastic decrease of the maximum lateral strengths and ductility. Since many factors may affect the installation of a post-installed anchor, it is better to use standard hooks to replace post-installed anchors in some specific points when using RC jacketing or installing wing walls.

  9. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.

    PubMed

    Valentin, Jan B; Andreetta, Christian; Boomsma, Wouter; Bottaro, Sandro; Ferkinghoff-Borg, Jesper; Frellsen, Jes; Mardia, Kanti V; Tian, Pengfei; Hamelryck, Thomas

    2014-02-01

    We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications.

  10. Detailed design of an SMA-actuated self-locking device for rotary feed structure

    NASA Astrophysics Data System (ADS)

    Xiaoyu, Qin; Xiaojun, Yan; Xiaoyong, Zhang; Weibing, Wang; Lianghai, Li

    2016-03-01

    This paper presents a detailed design of a locking device which is used to lock the rotary feed structure of a space-borne microwave radiometer during the launching stage. This locking device employs two redundant shape memory alloy (SMA) wires as the actuating elements, uses a self-locking structure to achieve the locking function and a step structure to ensure a safety clearance after release. Based on the design concept, preliminary design of the locking/release unit and the clamp unit are performed. Then, a more accurate simulation of the release process and the cyclic property of the device is carried out by using an improved Brinson’s SMA constitutive model and a heat transfer equation. After the design and simulation, four prototypes are fabricated and their performance tests are carried out to evaluate the self-locking property, lifetime and thermal tolerance.

  11. Structural flyby characterization of nanoporosity

    NASA Astrophysics Data System (ADS)

    Rosa, R. R.; Ferreira da Silva, A.; Brito, R. C.; Roman, L. S.; Baroni, M. P. M. A.; Ramos, F. M.; Ahuja, R.; Persson, C.

    2004-08-01

    Recently, Ferreira da Silva et al. [3] have performed a gradient pattern analysis of a canonical sample set (CSS) of scanning force microscopy (SFM) images of p-Si. They applied the so-called Gradient Pattern Analysis to images of three typical p-Si samples distinguished by different absorption energy levels and aspect ratios. Taking into account the measures of spatial asymmetric fluctuations they interpreted the global porosity not only in terms of the amount of roughness, but rather in terms of the structural complexity (e.g., walls and fine structures as slots). This analysis has been adapted in order to operate in a OpenGL flyby environment (the StrFB code), whose application give the numerical characterization of the structure during the flyby real time. Using this analysis we compare the levels of asymmetric fragmentation of active porosity related to different materials as p-Si and "porous diamond-like" carbon. In summary we have shown that the gradient pattern analysis technique in a flyby environment is a reliable sensitive method to investigate, qualitatively and quantitatively, the complex morphology of active nanostructures.

  12. The E-ELT project: the telescope main structure detailed design study

    NASA Astrophysics Data System (ADS)

    Marchiori, Gianpietro; Busatta, Andrea; Ghedin, Leonardo; De Lorenzi, Simone

    2012-09-01

    The European Extremely Large Telescope (E-ELT) is the biggest telescope in the world. Within the Detailed Design activities, ESO has awarded EIE GROUP (European Industrial Engineering) a contract for the Design of the Main Structure to the point where the concept of the telescope has been consolidated, from a construction point of view. All the Design activities have been developed in order to create an integrated system in terms of functionality and performance, while the engineering activities have been performed with the aim of obtaining a telescope that can be built, transported, integrated, with a reduced maintainability.

  13. A detailed Raman and X-ray study of UO2+x oxides and related structure transitions.

    PubMed

    Elorrieta, J M; Bonales, L J; Rodríguez-Villagra, N; Baonza, V G; Cobos, J

    2016-10-12

    This work presents a detailed study of hyperstoichiometric UO2+x (0 < x < 0.25) oxides and an assessment of the structural evolution taking place as oxidation proceeds. For this purpose, different UO2+x powder samples with controlled degree of non-stoichiometry have been identified by thermogravimetric analysis and characterized by X-ray diffraction (XRD) and Raman spectroscopy. XRD analysis reflects that the commonly assumed Vegard's law is not applicable over the whole hyperstoichiometry range, since a slight increase of the lattice constant is observed for 0.13 < x < 0.20. A quantitative Raman analysis of the UO2+x spectra as a function of the oxidation degree is also shown. A new method to characterize any UO2+x sample (for x < 0.20), based on the shift of the 630 cm(-1) band observed in the Raman spectrum, is proposed here for the first time. Moreover, three structure transitions have been detected at x = 0.05, 0.11 and 0.20, giving rise to four distinct regions associated with consecutive structural rearrangements over the hyperstoichiometry range: x < 0.05, 0.05 < x < 0.11, 0.11 < x < 0.20 and 0.20 < x < 0.25.

  14. Mineralogy of the SAFOD Main Hole: Detailed characterization of fault and country rocks

    NASA Astrophysics Data System (ADS)

    Solum, J. G.; Hickman, S. H.; Lockner, D. A.; Moore, D. E.

    2005-12-01

    Cuttings and core collected from across the San Andreas Fault Zone in the SAFOD Main Hole provide a unique opportunity to characterize the composition and structure of a major plate-boundary fault system. X-ray diffraction techniques provide a means to determine fault rock mineral assemblages, as well as help to identify the sedimentary packages that were encountered during drilling. These analyses indicate that there are multiple types of mineral assemblages in the fault rocks encountered by the SAFOD hole. Two zones of laumontite (zeolite) mineralization are present, one in the granodiorite encountered from ~244-1923 m (800 to 6310 ft) measured depth (MD), and one in a deeper arkose at ~2682 to 3158 m (~8800 to 10,360 ft) MD. Trace amounts of laumontite are associated with a possible shear zone at ~3338 m (10,950 ft) MD, but no clear relation between zeolite mineralization and other shear zones penetrated by SAFOD has been observed. The main hole entered a sequence of shale/siltstone/fine sandstones at ~3158 m (10360 ft) MD, indicating the presence of a significant fault. Below this depth the chlorite (001) XRD peak widths exhibit little variability (~0.35-0.4 compared to a broad range of ~0.15-0.6 above that depth), indicating a major change in lithology. There is also a very pronounced change in the clay mineral assemblages at ~3353 m (11000 ft) MD, below which clays (chlorite, illite, and a possible mixed-layer phase) exhibit little variation both in abundance and crystallinity, indicating the presence of a significant fault at approximately that depth. This is broadly consistent with the first appearance of serpentinite minerals at ~3322 m (10900 ft) MD, and a sudden increase in the concentration of methane dissolved in the drilling mud at 3338-3344 m (10950-10970 ft) MD. A mixed-layer illite-smectite phase is present in a major fault zone at ~2554 m (8380 ft) MD. This phase is present both in bulk cuttings as well as in plucked grains of fault rocks

  15. High-resolution crystal structure reveals molecular details of target recognition by bacitracin

    PubMed Central

    Economou, Nicoleta J.; Cocklin, Simon; Loll, Patrick J.

    2013-01-01

    Bacitracin is a metalloantibiotic agent that is widely used as a medicine and feed additive. It interferes with bacterial cell-wall biosynthesis by binding undecaprenyl-pyrophosphate, a lipid carrier that serves as a critical intermediate in cell wall production. Despite bacitracin’s broad use, the molecular details of its target recognition have not been elucidated. Here we report a crystal structure for the ternary complex of bacitracin A, zinc, and a geranyl-pyrophosphate ligand at a resolution of 1.1 Å. The antibiotic forms a compact structure that completely envelopes the ligand’s pyrophosphate group, together with flanking zinc and sodium ions. The complex adopts a highly amphipathic conformation that offers clues to antibiotic function in the context of bacterial membranes. Bacitracin’s efficient sequestration of its target represents a previously unseen mode for the recognition of lipid pyrophosphates, and suggests new directions for the design of next-generation antimicrobial agents. PMID:23940351

  16. Detailed analysis of surface asperity deformation mechanism in diffusion bonding of steel hollow structural components

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Li, H.; Li, M. Q.

    2016-05-01

    This study focused on the detailed analysis of surface asperity deformation mechanism in similar diffusion bonding as well as on the fabrication of high quality martensitic stainless steel hollow structural components. A special surface with regular patterns was processed to be joined so as to observe the extent of surface asperity deformation under different bonding pressures. Results showed that an undamaged hollow structural component has been obtained with full interfacial contact and the same shear strength to that of base material. Fracture surface characteristic combined with surface roughness profiles distinctly revealed the enhanced surface asperity deformation as the applied pressure increases. The influence of surface asperity deformation mechanism on joint formation was analyzed: (a) surface asperity deformation not only directly expanded the interfacial contact areas, but also released deformation heat and caused defects, indirectly accelerating atomic diffusion, then benefits to void shrinkage; (b) surface asperity deformation readily introduced stored energy difference between two opposite sides of interface grain boundary, resulting in strain induced interface grain boundary migration. In addition, the influence of void on interface grain boundary migration was analyzed in detail.

  17. Damping characterization in large structures

    NASA Technical Reports Server (NTRS)

    Eke, Fidelis O.; Eke, Estelle M.

    1991-01-01

    This research project has as its main goal the development of methods for selecting the damping characteristics of components of a large structure or multibody system, in such a way as to produce some desired system damping characteristics. The main need for such an analytical device is in the simulation of the dynamics of multibody systems consisting, at least partially, of flexible components. The reason for this need is that all existing simulation codes for multibody systems require component-by-component characterization of complex systems, whereas requirements (including damping) often appear at the overall system level. The main goal was met in large part by the development of a method that will in fact synthesize component damping matrices from a given system damping matrix. The restrictions to the method are that the desired system damping matrix must be diagonal (which is almost always the case) and that interbody connections must be by simple hinges. In addition to the technical outcome, this project contributed positively to the educational and research infrastructure of Tuskegee University - a Historically Black Institution.

  18. Crystal Structures of a Poplar Xyloglucan Endotransglycosylase Reveal Details of Transglycosylation Acceptor Binding

    PubMed Central

    Johansson, Patrik; Brumer, Harry; Baumann, Martin J.; Kallas, Åsa M.; Henriksson, Hongbin; Denman, Stuart E.; Teeri, Tuula T.; Jones, T. Alwyn

    2004-01-01

    Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Thus, XET is a key enzyme in all plant processes that require cell wall remodeling. To provide a basis for detailed structure–function studies, the crystal structure of Populus tremula x tremuloides XET16A (PttXET16A), heterologously expressed in Pichia pastoris, has been determined at 1.8-Å resolution. Even though the overall structure of PttXET16A is a curved β-sandwich similar to other enzymes in the glycoside hydrolase family GH16, parts of its substrate binding cleft are more reminiscent of the distantly related family GH7. In addition, XET has a C-terminal extension that packs against the conserved core, providing an additional β-strand and a short α-helix. The structure of XET in complex with a xyloglucan nonasaccharide, XLLG, reveals a very favorable acceptor binding site, which is a necessary but not sufficient prerequisite for transglycosylation. Biochemical data imply that the enzyme requires sugar residues in both acceptor and donor sites to properly orient the glycosidic bond relative to the catalytic residues. PMID:15020748

  19. Porous electrode apparatus for electrodeposition of detailed metal structures or microelectronic interconnections

    DOEpatents

    Griffiths, Stewart K.; Nilson, Robert H.; Hruby, Jill M.

    2002-01-01

    An apparatus and procedure for performing microfabrication of detailed metal structures by electroforming metal deposits within small cavities. Two primary areas of application are: the LIGA process which manufactures complex three-dimensional metal parts and the damascene process used for electroplating line and via interconnections of microelectronic devices. A porous electrode held in contact or in close proximity with a plating substrate or mold top to ensure one-dimensional and uniform current flow into all mold cavities is used. Electrolyte is pumped over the exposed surface of the porous electrode to ensure uniform ion concentrations at this external surface. The porous electrode prevents electrolyte circulation within individual mold cavities, avoiding preferential enhancement of ion transport in cavities having favorable geometries. Both current flow and ion transport are one-dimensional and identical in all mold cavities, so all metal deposits grow at the same rate eliminating nonuniformities of the prior art.

  20. Digital ultrasonic signal processing: Primary ultrasonics task and transducer characterization use and detailed description

    NASA Technical Reports Server (NTRS)

    Hammond, P. L.

    1979-01-01

    This manual describes the use of the primary ultrasonics task (PUT) and the transducer characterization system (XC) for the collection, processing, and recording of data received from a pulse-echo ultrasonic system. Both PUT and XC include five primary functions common to many real-time data acquisition systems. Some of these functions are implemented using the same code in both systems. The solicitation and acceptance of operator control input is emphasized. Those operations not under user control are explained.

  1. Detailed characterization of a highly Yb-doped double-clad fiber

    NASA Astrophysics Data System (ADS)

    Vallés, J. A.; Berdejo, V.; Martín, J. C.; Cases, R.; Álvarez, J. M.; Rebolledo, M. Á.

    2016-12-01

    A characterization method based on the careful measurement of the characteristic parameters and fluorescence emission spectra of a highly Yb-doped double-clad fiber is presented. The method is successfully checked by numerically fitting experimental results of a ring laser based on highly doped double-clad Yb-doped silica fibers with different dopant concentrations, fiber lengths and ring-laser output-coupler rates.

  2. Coupling gas chromatography and electronic nose detection for detailed cigarette smoke aroma characterization.

    PubMed

    Rambla-Alegre, Maria; Tienpont, Bart; Mitsui, Kazuhisa; Masugi, Eri; Yoshimura, Yuta; Nagata, Hisanori; David, Frank; Sandra, Pat

    2014-10-24

    Aroma characterization of whole cigarette smoke samples using sensory panels or electronic nose (E-nose) devices is difficult due to the masking effect of major constituents and solvent used for the extraction step. On the other hand, GC in combination with olfactometry detection does not allow to study the delicate balance and synergetic effect of aroma solutes. To overcome these limitations a new instrumental set-up consisting of heart-cutting gas chromatography using a capillary flow technology based Deans switch and low thermal mass GC in combination with an electronic nose device is presented as an alternative to GC-olfactometry. This new hyphenated GC-E-nose configuration is used for the characterization of cigarette smoke aroma. The system allows the transfer, combination or omission of selected GC fractions before injection in the E-nose. Principal component analysis (PCA) and discriminant factor analysis (DFA) allowed clear visualizing of the differences among cigarette brands and classifying them independently of their nicotine content. Omission and perceptual interaction tests could also be carried out using this configuration. The results are promising and suggest that the GC-E-nose hyphenation is a good approach to measure the contribution level of individual compounds to the whole cigarette smoke.

  3. A new Monte Carlo method for investigating geometrical structures of lipid membranes with atomistic detail

    NASA Astrophysics Data System (ADS)

    Cheng, Sara; Qiu, Liming; Cheng, K.; Vaughn, Mark

    2011-10-01

    The distribution statistics of the surface area, volume and voids of lipid molecules are important parameters to characterize the structures of self-assembling lipid membranes. Traditional methods are mostly based on various assumptions of the thickness of the lipid membrane and the volumes of certain types of lipid molecules. However, those methods usually lead to an over- or underestimation of the average surface area of lipid molecules when compared to the experimental results of the pure lipid systems. We developed a new Monte Carlo method that is able to estimate the distributions and averages of surface area, volume and void space of the lipid molecules in the absence and presence of proteins of the MD simulation results of lipid membranes at the atomistic scale. We successfully validated our new method on an ordered hard-sphere system and on a phospholipid/cholesterol binary lipid system, all with known structural parameters. Using this new method, the structural perturbation of the conformal annular lipids in close proximity to the embedded protein in a lipid/protein system will also be presented.

  4. Beyond Flood Hazard Maps: Detailed Flood Characterization with Remote Sensing, GIS and 2d Modelling

    NASA Astrophysics Data System (ADS)

    Santillan, J. R.; Marqueso, J. T.; Makinano-Santillan, M.; Serviano, J. L.

    2016-09-01

    Flooding is considered to be one of the most destructive among many natural disasters such that understanding floods and assessing the risks associated to it are becoming more important nowadays. In the Philippines, Remote Sensing (RS) and Geographic Information System (GIS) are two main technologies used in the nationwide modelling and mapping of flood hazards. Although the currently available high resolution flood hazard maps have become very valuable, their use for flood preparedness and mitigation can be maximized by enhancing the layers of information these maps portrays. In this paper, we present an approach based on RS, GIS and two-dimensional (2D) flood modelling to generate new flood layers (in addition to the usual flood depths and hazard layers) that are also very useful in flood disaster management such as flood arrival times, flood velocities, flood duration, flood recession times, and the percentage within a given flood event period a particular location is inundated. The availability of these new layers of flood information are crucial for better decision making before, during, and after occurrence of a flood disaster. The generation of these new flood characteristic layers is illustrated using the Cabadbaran River Basin in Mindanao, Philippines as case study area. It is envisioned that these detailed maps can be considered as additional inputs in flood disaster risk reduction and management in the Philippines.

  5. Hydrodynamic Characterization of Harmonically Excited Falling-Films: A Detailed Experimental and Computational Study

    NASA Astrophysics Data System (ADS)

    Charogiannis, Alexandros; Denner, Fabian; van Wachem, Berend; Pradas, Marc; Kalliadasis, Serafim; Markides, Christos

    2016-11-01

    We investigate the hydrodynamic characteristics of harmonically excited liquid-films flowing down a 20circ; incline by simultaneous application of Particle Tracking Velocimetry and Planar Laser-Induced Fluorescence (PLIF) imaging, complemented by Direct Numerical Simulations. By simultaneously implementing the above two optical techniques, instantaneous and highly localised flow-rate data were also retrieved, based on which the effect of local film topology on the flow-field underneath the wavy interface is studied in detail. Our main result is that the instantaneous flow rate varies linearly with the instantaneous film-height, as confirmed by both experiments and simulations. Furthermore, both experimental and numerical flow-rate data are closely approximated by a simple analytical relationship, which is reported here for the first time, with only minor deviations. This relationship includes the wave speed c and mean flow-rate Q , both of which can be obtained by simple and inexpensive measurement techniques, thus allowing for spatiotemporally resolved flow-rate predictions to be made without requiring any knowledge of the full flow-field from below the wavy interface.

  6. Detailed characterization of power flow and PRS performance on Phoenix. Memorandum report

    SciTech Connect

    Terry, R.E.; Whitney, K.G.; Davis, J.; Guiliani, J.L.; Rogerson, J.

    1996-05-03

    This study first constructs a complete model of the Phoenix pulser and its puff gas load, connects the model with experimental findings, and then suggests some means of improving the pulser`s K shell x-ray yield. A numerical study of energy coupling into a dummy resistive load showed that an output impedance of about 1 omega would minimize the reflected energy; from this result a thevenin equivalent circuit was constructed. Use of the transmission line model to study the Phoenix pre-pulse evolved to a study of early power flow and has produced a breakdown model that contains a detailed field map for the PRS load cavity, a mapping of the computed electric field values onto the grid of neutral gas density measurements, and a simple ionization model. Preliminary results from the breakdown model indicate ionization regions consistent with the observed `reversed` zippering, and a Boltzmann solution in those regions shows that at 40% of peak field the ionization would proceed in about 6 ns. A series of full 1D MHD studies, equipped with both CRE and time dependent ionization and excited state models, has refined the expected yields for Ar gas to about 18 kJ using a 4 cm long, shell of 0.375 mgm mass.

  7. Possibility of supervision over detailed structure of ocean currents by MODIS

    NASA Astrophysics Data System (ADS)

    Sklyarov, V. E.

    2008-02-01

    The report focuses on the analysis of the detail structure of ocean currents in areas of dust storms distribution or intensive phytoplankton's development. Dust storms represent the global phenomenon occurring regularly and, thus, atmospheric streams transfer a significant amount of the sand and dust (more than 2000 million tons) from deserts of Gobi, Sahara, Namibia, and Arabian Peninsula etc. The dust from Sahara achieves Caribbean Sea and southeast areas of USA for 5-7 days, and traces of the Asian dust storm, which have crossed Pacific Ocean, were found out in Great Lakes. For the purposes of our research the influence of sand and a dust dropping out from atmosphere on optical properties of the top layer of the ocean is represented especially significant. We shall note, that this question is poorly covered in the scientific literature. On our data, there are only separate certificates that return dispersion in green area of a spectrum for the top layer of the ocean is considerably increased after passage of a dust storm. It occurs due to saturation of the ocean top layer sand particles were sunlight diffusion is good. On the other hand, these particles, being a passive tracer, are easily involved by separate jets of currents in local circulation. These factors create a real basis for space observations on details mesoscale ocean circulation. As a trial experiment, author of the report have leaded the multispectral analysis data from MODIS (satellite AQUA), received on a northwest part Indian Ocean and Gulf of Aden. Results of the analysis confirm the made hypothesis.

  8. Simulating photon scattering effects in structurally detailed ventricular models using a Monte Carlo approach.

    PubMed

    Bishop, Martin J; Plank, Gernot

    2014-01-01

    Light scattering during optical imaging of electrical activation within the heart is known to significantly distort the optically-recorded action potential (AP) upstroke, as well as affecting the magnitude of the measured response of ventricular tissue to strong electric shocks. Modeling approaches based on the photon diffusion equation have recently been instrumental in quantifying and helping to understand the origin of the resulting distortion. However, they are unable to faithfully represent regions of non-scattering media, such as small cavities within the myocardium which are filled with perfusate during experiments. Stochastic Monte Carlo (MC) approaches allow simulation and tracking of individual photon "packets" as they propagate through tissue with differing scattering properties. Here, we present a novel application of the MC method of photon scattering simulation, applied for the first time to the simulation of cardiac optical mapping signals within unstructured, tetrahedral, finite element computational ventricular models. The method faithfully allows simulation of optical signals over highly-detailed, anatomically-complex MR-based models, including representations of fine-scale anatomy and intramural cavities. We show that optical action potential upstroke is prolonged close to large subepicardial vessels than further away from vessels, at times having a distinct "humped" morphology. Furthermore, we uncover a novel mechanism by which photon scattering effects around vessels cavities interact with "virtual-electrode" regions of strong de-/hyper-polarized tissue surrounding cavities during shocks, significantly reducing the apparent optically-measured epicardial polarization. We therefore demonstrate the importance of this novel optical mapping simulation approach along with highly anatomically-detailed models to fully investigate electrophysiological phenomena driven by fine-scale structural heterogeneity.

  9. Simulating photon scattering effects in structurally detailed ventricular models using a Monte Carlo approach

    PubMed Central

    Bishop, Martin J.; Plank, Gernot

    2014-01-01

    Light scattering during optical imaging of electrical activation within the heart is known to significantly distort the optically-recorded action potential (AP) upstroke, as well as affecting the magnitude of the measured response of ventricular tissue to strong electric shocks. Modeling approaches based on the photon diffusion equation have recently been instrumental in quantifying and helping to understand the origin of the resulting distortion. However, they are unable to faithfully represent regions of non-scattering media, such as small cavities within the myocardium which are filled with perfusate during experiments. Stochastic Monte Carlo (MC) approaches allow simulation and tracking of individual photon “packets” as they propagate through tissue with differing scattering properties. Here, we present a novel application of the MC method of photon scattering simulation, applied for the first time to the simulation of cardiac optical mapping signals within unstructured, tetrahedral, finite element computational ventricular models. The method faithfully allows simulation of optical signals over highly-detailed, anatomically-complex MR-based models, including representations of fine-scale anatomy and intramural cavities. We show that optical action potential upstroke is prolonged close to large subepicardial vessels than further away from vessels, at times having a distinct “humped” morphology. Furthermore, we uncover a novel mechanism by which photon scattering effects around vessels cavities interact with “virtual-electrode” regions of strong de-/hyper-polarized tissue surrounding cavities during shocks, significantly reducing the apparent optically-measured epicardial polarization. We therefore demonstrate the importance of this novel optical mapping simulation approach along with highly anatomically-detailed models to fully investigate electrophysiological phenomena driven by fine-scale structural heterogeneity. PMID:25309442

  10. Incorporating Detailed Chemical Characterization of Biomass Burning Emissions into Air Quality Models

    NASA Astrophysics Data System (ADS)

    Barsanti, K.; Hatch, L. E.; Yokelson, R. J.; Stockwell, C.; Orlando, J. J.; Emmons, L. K.; Knote, C. J.; Wiedinmyer, C.

    2015-12-01

    Approximately 500 Tg/yr of non-methane organic compounds (NMOCs) are emitted by biomass burning (BB) to the global atmosphere, leading to the photochemical production of ozone (O3) and secondary particulate matter (PM). Until recently, in studies of BB emissions, a significant mass fraction of NMOCs (up to 80%) remained uncharacterized or unidentified. Models used to simulate the air quality impacts of BB thus have relied on very limited chemical characterization of the emitted compounds. During the Fourth Fire Lab at Missoula Experiment (FLAME-IV), an unprecedented fraction of emitted NMOCs were identified and quantified through the application of advanced analytical techniques. Here we use FLAME-IV data to improve BB emissions speciation profiles for individual fuel types. From box model simulations we evaluate the sensitivity of predicted precursor and pollutant concentrations (e.g., formaldehyde, acetaldehyde, and terpene oxidation products) to differences in the emission speciation profiles, for a range of ambient conditions (e.g., high vs. low NOx). Appropriate representation of emitted NMOCs in models is critical for the accurate prediction of downwind air quality. Explicit simulation of hundreds of NMOCs is not feasible; therefore we also investigate the consequences of using existing assumptions and lumping schemes to map individual NMOCs to model surrogates and we consider alternative strategies. The updated BB emissions speciation profiles lead to markedly different surrogate compound distributions than the default speciation profiles, and box model results suggest that these differences are likely to affect predictions of PM and important gas-phase species in chemical transport models. This study highlights the potential for further BB emissions characterization studies, with concerted model development efforts, to improve the accuracy of BB predictions using necessarily simplified mechanisms.

  11. Automated Characterization Of Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Yam, Yeung; Mettler, Edward; Hadaegh, Fred Y.; Milman, Mark H.; Scheid, Robert E.

    1992-01-01

    Automated method of characterizing dynamical properties of large flexible structure yields estimates of modal parameters used by robust control system to stabilize structure and minimize undesired motions. Based on extraction of desired modal and control-design data from responses of structure to known vibrational excitations. Applicable to terrestrial structures where vibrations are important - aircraft, buildings, bridges, cranes, and drill strings.

  12. Processing of Uav Based Range Imaging Data to Generate Detailed Elevation Models of Complex Natural Structures

    NASA Astrophysics Data System (ADS)

    Kohoutek, T. K.; Eisenbeiss, H.

    2012-07-01

    Unmanned Aerial Vehicles (UAVs) are more and more used in civil areas like geomatics. Autonomous navigated platforms have a great flexibility in flying and manoeuvring in complex environments to collect remote sensing data. In contrast to standard technologies such as aerial manned platforms (airplanes and helicopters) UAVs are able to fly closer to the object and in small-scale areas of high-risk situations such as landslides, volcano and earthquake areas and floodplains. Thus, UAVs are sometimes the only practical alternative in areas where access is difficult and where no manned aircraft is available or even no flight permission is given. Furthermore, compared to terrestrial platforms, UAVs are not limited to specific view directions and could overcome occlusions from trees, houses and terrain structures. Equipped with image sensors and/or laser scanners they are able to provide elevation models, rectified images, textured 3D-models and maps. In this paper we will describe a UAV platform, which can carry a range imaging (RIM) camera including power supply and data storage for the detailed mapping and monitoring of complex structures, such as alpine riverbed areas. The UAV platform NEO from Swiss UAV was equipped with the RIM camera CamCube 2.0 by PMD Technologies GmbH to capture the surface structures. Its navigation system includes an autopilot. To validate the UAV-trajectory a 360° prism was installed and tracked by a total station. Within the paper a workflow for the processing of UAV-RIM data is proposed, which is based on the processing of differential GNSS data in combination with the acquired range images. Subsequently, the obtained results for the trajectory are compared and verified with a track of a UAV (Falcon 8, Ascending Technologies) carried out with a total station simultaneously to the GNSS data acquisition. The results showed that the UAV's position using differential GNSS could be determined in the centimetre to the decimetre level. The RIM

  13. Detailed characterizations of the new Mines Douai comparative reactivity method instrument via laboratory experiments and modeling

    NASA Astrophysics Data System (ADS)

    Michoud, V.; Hansen, R. F.; Locoge, N.; Stevens, P. S.; Dusanter, S.

    2015-08-01

    The hydroxyl (OH) radical is an important oxidant in the troposphere, which controls the lifetime of most air quality- and climate-related trace gases. However, there are still uncertainties concerning its atmospheric budget, and integrated measurements of OH sinks have been valuable to improve this aspect. Among the analytical tools used for measuring total OH reactivity in ambient air, the comparative reactivity method (CRM) is spreading rapidly in the atmospheric community. However, measurement artifacts have been highlighted for this technique, and additional work is needed to fully characterize them. In this study, we present the new Mines Douai CRM instrument, with an emphasis on the corrections that need to be applied to ambient measurements of total OH reactivity. Measurement artifacts identified in the literature have been investigated, including (1) a correction for a change in relative humidity between the measurement steps leading to different OH levels, (2) the formation of spurious OH in the sampling reactor when hydroperoxy radicals (HO2) react with nitrogen monoxide (NO), (3) not operating the CRM under pseudo-first-order kinetics, and (4) the dilution of ambient air inside the reactor. The dependences of these artifacts on various measurable parameters, such as the pyrrole-to-OH ratio and the bimolecular reaction rate constants of ambient trace gases with OH, have also been studied. Based on these observations, parameterizations are proposed to correct ambient OH reactivity measurements. On average, corrections of 5.2 ± 3.2, 9.2 ± 15.7, and 8.5 ± 5.8 s-1 were respectively observed for (1), (2) and (3) during a field campaign performed in Dunkirk, France (summer 2014). Numerical simulations have been performed using a box model to check whether experimental observations mentioned above are consistent with our understanding of the chemistry occurring in the CRM reactor. Two different chemical mechanisms have been shown to reproduce the magnitude

  14. Detailed Characterization of aerosol properties from satellite Observations using GRASP algorithm

    NASA Astrophysics Data System (ADS)

    Dubovik, O.; Litvinov, P.; Lapyonok, T.; Ducos, F.; Huang, X.; Lopatin, A.; Fuertes, D.; Torres, B.

    2015-12-01

    GRASP (Generalized Retrieval of Aerosol and Surface Properties) is rather sophisticated algorithm was developed recently by Dubovik et al. (2011, 2014) with objective of achieving more complete and accurate aerosols and surface retrieval. Specifically, GPASP searches in continuous space of solutions and doesn't utilize look-up-tables. It based on highly elaborated statistically optimized fitting. For example, it uses multi-pixel retrieval when statistically optimized inversion is implemented simultaneously for a group of satellite pixels. This allows using additional a priori information about limited variability of aerosol of surface properties in time and/or space. As a result, GRASP doesn't use any specific information about aerosol or surface type in the each observed pixel, and the results are essentially driven by observations. However GRASP retrieval takes longer computational time compare to most conventional algorithms that is the main practical challenge of employing GRASP for massive data processing. Nonetheless, in last two years, GRASP has been significantly optimized and adapted to operational needs. As a result of this optimization, GRASP has been accelerated to the level acceptable for processing large volumes of satellite observations. Recently GRASP has been applied to multi-years archives of PARASO/POLDER and ENVISAT/MERIS. Based, on the preliminary analysis GRASP results are very promising for comprehensive characterization of aerosol even for observations over bright surfaces and for monitoring very high aerosol loading events (with AOD 2 or 3). In addition, it was made the attempts to estimate such aerosol characteristics as aerosol height, air mass, radiative forcing, aerosol type, etc. The results and illustrations will be presented.

  15. Detailed PCB congener characterization of influent and effluent at New York and New Jersey WPCPs

    SciTech Connect

    Durell, G.S.; Lizotte, R.D. Jr.; Solomon, M.H.; Green, J.W.; Spadone, J.; Pires, L.

    1995-12-31

    The waste streams at 26 New York City and New Jersey water pollution control plants (WPCP) were characterized for PCB. Time-integrated influent and effluent samples were collected during normal and high (storm) flow conditions; high flow influent simulated what may by-pass the plant and be discharged through combined sewer overflows. State-of-the-art congener-specific analytical methods were used to achieve detection limits from 0.05 to 0.3 ng/L. Concentrations of 71 individual PCB congeners that constitute approximately 95% of the total PCB in Aroclors and environmental samples were determined. The PCB concentrations and congener distributions varied notably among plants. Individual congener concentrations were typically well below 1 ng/L in the effluent, with a few congeners being detected at 5 to 10 ng/L levels in some samples. The concentrations were under 1 ng/L in most influent samples, with occasional determinations above 10 ng/L. The average total PCB concentration, defined as the sum of the 71 individual congener concentrations, at the 26 WPCPs were 27, 110, and 160 ng/L for normal flow effluent, normal flow influent, and high flow influent, respectively. The results indicate that PCB levels in New York City and New Jersey WPCP discharges are generally low, with most effluent having total PCB concentrations below 0.05 {micro}g/L. The PCB levels in the influent were commonly under 0.1 {micro}g/L and became slightly elevated at most plants during storms while at some plants the increase in flow appeared to dilute the PCB in the influent. The WPCPs remove, on average, approximately 75% of the PCB received in the influent.

  16. The detailed crystal and electronic structures of the cotunnite-type ZrO2

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Duan, Li; Ji, Vincent

    2016-07-01

    The detailed crystal and orbital-decomposed electronic structures of cotunnite-type ZrO2 have been investigated by using the first-principles projector augmented wave (PAW) potential within the generalized gradient approximation as well as taking into account on-site Coulomb repulsive interaction (GGA+U). The optimized structure shows that the OI and OII anions are surrounded by an arbitrary tetrahedron of four Zr cations and an arbitrary pentahedron of five Zr cations, respectively, in turn, the Zr cation is surrounded by an arbitrary tetrakaidecahedron formed by nine oxygen ligands. Although one more Zr cation is coordinated to OII, the larger bond lengths between OII and its adjacent five Zr cations (dOII-Zr) than those between OI and its adjacent four Zr cations (dOI-Zr) makes density of states (DOS) of s and three p (px , py and pz) states of the OII anion driving down in lower energy region and driving up in higher energy region. No crystal-field splitting is observed between three p (px , py and pz) states of anions OI and OII (between three p (px , py and pz) states and five d (dxy , dyz , dxz , dz2 and dx2-y2) states of cation Zr) is resulted from the arrangements of the surrounding cations (anions) do not have any symmetry. The additional covalent character upon Zr-O ionic bonds is attributed to the hybridization of itinerant Zr(5s) and less filled Zr(4d) states to the separated O(2s) and O(2p) states.

  17. Numerical prediction of oblique detonation wave structures using detailed and reduced reaction mechanisms

    NASA Astrophysics Data System (ADS)

    Thaker, A. A.; Chelliah, H. K.

    1997-12-01

    Modelling of the structure and the limiting flow turning angles of an oblique detonation wave, established by a two-dimensional wedge, requires the implementation of detailed chemical kinetic models involving a large number of chemical species. In this paper, a method of reducing the computational effort involved in simulating such high-speed reacting flows by implementing a systematically reduced reaction mechanism is presented. For a hydrogen - air mixture, starting with an elementary mechanism having eight species in 12 reactions, three alternate four-step reduced reaction mechanisms are developed by introducing the steady-state approximation for the reaction intermediates HO2, O and OH, respectively. Additional reduction of the computational effort is achieved by introducing simplifications to the thermochemical data evaluations. The influence of the numerical grid used in predicting the induction process behind the shock is also investigated. Comparisons of the induction zone predicted by two-dimensional oblique detonation wave calculations with that of a static reactor model (with initial conditions of the gas mixture specified by those behind the nonreactive oblique shock wave) are also presented. The reasonably good agreement between the three four-step reduced mechanism predictions and the starting mechanism predictions indicates that further reduction to a two-step mechanism is feasible for the physical flow time scales (corresponding to inflow Mach numbers of 8 - 10) considered here, and needs to be pursued in the future.

  18. Water replacement hypothesis in atomic detail--factors determining the structure of dehydrated bilayer stacks.

    PubMed

    Golovina, Elena A; Golovin, Andrey V; Hoekstra, Folkert A; Faller, Roland

    2009-07-22

    According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (<1:1, 1:1, and >1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar "stacks" through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis.

  19. Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

    PubMed Central

    Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

    2003-01-01

    The conformational space of the 10–55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP/3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 Å and 4.54 Å were obtained with SRFOPT and OONS, respectively. These results show that the protein-folding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information. PMID:14638943

  20. A global/local analysis method for treating details in structural design

    NASA Technical Reports Server (NTRS)

    Aminpour, Mohammad A.; Mccleary, Susan L.; Ransom, Jonathan B.

    1993-01-01

    A method for analyzing global/local behavior of plate and shell structures is described. In this approach, a detailed finite element model of the local region is incorporated within a coarser global finite element model. The local model need not be nodally compatible (i.e., need not have a one-to-one nodal correspondence) with the global model at their common boundary; therefore, the two models may be constructed independently. The nodal incompatibility of the models is accounted for by introducing appropriate constraint conditions into the potential energy in a hybrid variational formulation. The primary advantage of this method is that the need for transition modeling between global and local models is eliminated. Eliminating transition modeling has two benefits. First, modeling efforts are reduced since tedious and complex transitioning need not be performed. Second, errors due to the mesh distortion, often unavoidable in mesh transitioning, are minimized by avoiding distorted elements beyond what is needed to represent the geometry of the component. The method is applied reduced to a plate loaded in tension and transverse bending. The plate has a central hole, and various hole sixes and shapes are studied. The method is also applied to a composite laminated fuselage panel with a crack emanating from a window in the panel. While this method is applied herein to global/local problems, it is also applicable to the coupled analysis of independently modeled components as well as adaptive refinement.

  1. Detailed fault structure of the 2000 Western Tottori, Japan, earthquake sequence

    USGS Publications Warehouse

    Fukuyama, E.; Ellsworth, W.L.; Waldhauser, F.; Kubo, A.

    2003-01-01

    We investigate the faulting process of the aftershock region of the 2000 western Tottori earthquake (Mw 6.6) by combining aftershock hypocenters and moment tensor solutions. Aftershock locations were precisely determined by the double difference method using P- and S-phase arrival data of the Japan Meteorological Agency unified catalog. By combining the relocated hypocenters and moment tensor solutions of aftershocks by broadband waveform inversion of FREESIA (F-net), we successfully resolved very detailed fault structures activated by the mainshock. The estimated fault model resolves 15 individual fault segments that are consistent with both aftershock distribution and focal mechanism solutions. Rupture in the mainshock was principally confined to the three fault elements in the southern half of the zone, which is also where the earliest aftershocks concentrate. With time, the northern part of the zone becomes activated, which is also reflected in the postseismic deformation field. From the stress tensor analysis of aftershock focal mechanisms, we found a rather uniform stress field in the aftershock region, although fault strikes were scattered. The maximum stress direction is N107??E, which is consistent with the tectonic stress field in this region. In the northern part of the fault, where no slip occurred during the mainshock but postseismic slip was observed, the maximum stress direction of N130??E was possible as an alternative solution of stress tensor inversion.

  2. Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum.

    PubMed Central

    Berriman, M; Fairlamb, A H

    1998-01-01

    Cyclosporin (Cs) A has pronounced antimalarial activity in vitro and in vivo. In other organisms, the drug is thought to exert its effects either by inhibiting the peptidylprolyl cis/trans isomerase activity of cyclophilin (CyP) or by forming a CyP-CsA complex that inhibits the phosphatase activity of calcineurin. We have cloned and overexpressed in Escherichia coli a gene encoding a CyP from Plasmodium falciparum (PfCyP19) that is located on chromosome 3. The sequence of PfCyP19 shows remarkable sequence identity with human CyPA and, unlike the two previously identified CyPs from P. falciparum, PfCyP19 has no signal peptide or N-terminal sequence extension, suggesting a cytosolic localization. All the residues implicated in the recognition of the synthetic substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide are conserved, resulting in characteristically high Michaelis-Menten and specificity constants (Km>>120 microM, kcat/Km=1.2x10(7) M-1.s-1 respectively). As the first line in the functional characterization of this enzyme, we have assessed its binding affinity for CsA. In accordance with its tryptophan-containing CsA-binding domain, PfCyP19 binds CsA with high affinity (Kd=13 nM, Ki=6.9 nM). Twelve CsA analogues were also found to possess Ki values similar to CsA, with the notable exceptions of Val2-Cs (Ki=218 nM) and Thr2-Cs (Ki=690 nM). The immunosuppressants rapamycin and FK506 were inactive as inhibitors, consistent with other members of the CyP family of rotamases. The CsA analogues were also assessed as inhibitors of P. falciparum growth in vitro. Although their antimalarial activity did not correlate with inhibition of enzyme activity, residues 3 and 4 of CsA appeared to be important for inhibition of parasite growth and residues 1 and 2 for PfCyP19 inhibition. We propose that a malarial CyP-CsA complex presents residues 3 and 4 as part of an 'effector surface' for recognition by a downstream target, similar to the proposed mechanism for T

  3. Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail

    PubMed Central

    Zielińska, Joanna; Wieczór, Miłosz; Bączek, Tomasz; Gruszecki, Marcin; Czub, Jacek

    2016-01-01

    Amphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich) and mammalian (cholesterol-rich) membranes. In this work, we investigate the initial steps of AmB self-association by studying the structural, thermodynamic and spectral properties of AmB dimers in aqueous medium using molecular dynamics simulations. Our results show that in water, the hydrophobic aggregation of AmB monomers yields almost equiprobable populations of parallel and antiparallel dimers that rapidly interconvert into each other, and the dipole-dipole interaction between zwitterionic head groups plays a minor role in determining the drug’s tendency for self-aggregation. A simulation of circular dichroism (CD) spectra indicates that in experimental measurements, the signature CD spectrum of AmB aggregates should be attributed to higher-order oligomers rather than dimers. Finally, we suggest that oligomerization can impair the selectivity of AmB molecules for fungal membranes by increasing their hydrophobic drive for non-specific membrane insertion. PMID:26742886

  4. Detailed characterization of hyaluronan using aqueous size exclusion chromatography with triple detection and multiangle light scattering detection.

    PubMed

    Harmon, Patricia S; Maziarz, E Peter; Liu, X Michael

    2012-10-01

    Hyaluronan (HA) has attracted great interest and attention from ophthalmic surgical and eye care companies owing to its unique properties. A more complete understanding of HA biopolymers has, therefore, become increasingly critical as thorough characterization of raw materials helps promote product quality and process control. Often, such detailed information requires the use of a combination of analytical techniques. In this study, we compared size exclusion chromatography (SEC) with online multiangle light scattering (SEC-MALS) and SEC with triple detection (SEC-TD) experiments for HA analysis. Three lots of commercially available eye drop grade HA were characterized by SEC-MALS and SEC-TD. The absolute molecular weight averages, molecular weight distribution, radius of gyration, and solution conformation of the three HA lots were determined and compared by the two techniques. In addition, the intrinsic viscosity and intrinsic viscosity distribution were measured by SEC-TD.

  5. Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction

    PubMed Central

    Handl, Julia; Lovell, Simon C.

    2016-01-01

    ABSTRACT Energy functions, fragment libraries, and search methods constitute three key components of fragment‐assembly methods for protein structure prediction, which are all crucial for their ability to generate high‐accuracy predictions. All of these components are tightly coupled; efficient searching becomes more important as the quality of fragment libraries decreases. Given these relationships, there is currently a poor understanding of the strengths and weaknesses of the sampling approaches currently used in fragment‐assembly techniques. Here, we determine how the performance of search techniques can be assessed in a meaningful manner, given the above problems. We describe a set of techniques that aim to reduce the impact of the energy function, and assess exploration in view of the search space defined by a given fragment library. We illustrate our approach using Rosetta and EdaFold, and show how certain features of these methods encourage or limit conformational exploration. We demonstrate that individual trajectories of Rosetta are susceptible to local minima in the energy landscape, and that this can be linked to non‐uniform sampling across the protein chain. We show that EdaFold's novel approach can help balance broad exploration with locating good low‐energy conformations. This occurs through two mechanisms which cannot be readily differentiated using standard performance measures: exclusion of false minima, followed by an increasingly focused search in low‐energy regions of conformational space. Measures such as ours can be helpful in characterizing new fragment‐based methods in terms of the quality of conformational exploration realized. Proteins 2016; 84:411–426. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:26799916

  6. A detailed study of the structure of the nested planetary nebula, Hb 12, the Matryoshka nebula

    SciTech Connect

    Clark, D. M.; López, J. A.; Edwards, M. L.; Winge, C. E-mail: jal@astrosen.unam.mx E-mail: cwinge@gemini.edu

    2014-11-01

    We present near-IR, integral field spectroscopic observations of the planetary nebula (PN) Hb 12 using Near-infrared Integral Field Spectrograph (NIFS) on Gemini-North. Combining NIFS with the adaptive optics system Altair, we provide a detailed study of the core and inner structure of this PN. We focus the analysis in the prominent emission lines [Fe II] (1.6436 μm), He I (2.0585 μm), H{sub 2} (2.1214 μm), and Br{sub γ} (2.16553 μm). We find that the [Fe II] emission traces a tilted system of bipolar lobes, with the northern lobe being redshifted and the southern lobe blueshifted. The [Fe II] emission is very faint at the core and only present close to the systemic velocity. There is no H{sub 2} emission in the core, whereas the core is prominent in the He I and Br{sub γ} recombination lines. The H{sub 2} emission is concentrated in equatorial arcs of emission surrounding the core and expanding at ∼30 km s{sup –1}. These arcs are compared with Hubble Space Telescope images and shown to represent nested loops belonging to the inner sections of a much larger bipolar structure that replicates the inner one. The He I and Br{sub γ} emission from the core clearly show a cylindrical central cavity that seems to represent the inner walls of an equatorial density enhancement or torus. The torus is 0.''2 wide (≡200 AU radius at a distance of 2000 pc) and expanding at ≤30 km s{sup –1}. The eastern wall of the inner torus is consistently more intense than the western wall, which could indicate the presence of an off-center star, such as is observed in the similar hourglass PN, MyCn 18. A bipolar outflow is also detected in Br{sub γ} emerging within 0.''1 from the core at ∼ ± 40 km s{sup –1}.

  7. Solution Synchrotron X-ray Diffraction Reveals Structural Details of Lipid Domains in Ternary Mixtures

    SciTech Connect

    Yuan, J.; Kiss, A; Pramudya, Y; Nguyen, L; Hirst, L

    2009-01-01

    The influence of cholesterol on lipid bilayer structure is significant and the effect of cholesterol on lipid sorting and phase separation in lipid-raft-forming model membrane systems has been well investigated by microscopy methods on giant vesicles. An important consideration however is the influence of fluorescence illumination on the phase state of these lipids and this effect must be carefully minimized. In this paper, we show that synchrotron x-ray scattering on solution lipid mixtures is an effective alternative technique for the identification and characterization of the l o (liquid ordered) and l d (liquid disordered) phases. The high intensity of synchrotron x rays allows the observation of up to 5 orders of diffraction from the l o phase, whereas only two are clearly visible when the l d phase alone is present. This data can be collected in approximately 1 min/sample, allowing rapid generation of phase data. In this paper, we measure the lamellar spacing in both the liquid-ordered and liquid-disordered phases simultaneously, as a function of cholesterol concentration in two different ternary mixtures. We also observe evidence of a third gel-phaselike population at 10-12 mol % cholesterol and determine the thickness of the bilayer for this phase. Importantly we are able to look at phase coexistence in the membrane independent of photoeffects.

  8. Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction.

    PubMed

    Kandathil, Shaun M; Handl, Julia; Lovell, Simon C

    2016-04-01

    Energy functions, fragment libraries, and search methods constitute three key components of fragment-assembly methods for protein structure prediction, which are all crucial for their ability to generate high-accuracy predictions. All of these components are tightly coupled; efficient searching becomes more important as the quality of fragment libraries decreases. Given these relationships, there is currently a poor understanding of the strengths and weaknesses of the sampling approaches currently used in fragment-assembly techniques. Here, we determine how the performance of search techniques can be assessed in a meaningful manner, given the above problems. We describe a set of techniques that aim to reduce the impact of the energy function, and assess exploration in view of the search space defined by a given fragment library. We illustrate our approach using Rosetta and EdaFold, and show how certain features of these methods encourage or limit conformational exploration. We demonstrate that individual trajectories of Rosetta are susceptible to local minima in the energy landscape, and that this can be linked to non-uniform sampling across the protein chain. We show that EdaFold's novel approach can help balance broad exploration with locating good low-energy conformations. This occurs through two mechanisms which cannot be readily differentiated using standard performance measures: exclusion of false minima, followed by an increasingly focused search in low-energy regions of conformational space. Measures such as ours can be helpful in characterizing new fragment-based methods in terms of the quality of conformational exploration realized.

  9. Attenuation tomography in the western central Andes: A detailed insight into the structure of a magmatic arc

    NASA Astrophysics Data System (ADS)

    Haberland, Christian; Rietbrock, Andreas

    2001-06-01

    High-quality data from 1498 local earthquakes recorded by the PISCO '94 (Proyecto de Investigatión Sismológica de la Cordillera Occidental, 1994) and ANCORP '96 (Andean Continental Research Project, 1996) temporary seismological networks allowed the detailed determination of the three-dimensional (3-D) attenuation structure (Qp-1) beneath the recent magmatic arc in the western central Andes (20° to 24°S). Assuming a frequency-independent Qp-1 in a frequency band between 1 and 30 Hz, whole path attenuation (t*) was estimated from the amplitude spectra of the P waves using spectral ratios and a spectral inversion technique. The damped least squares inversion (tomography) of the data reveals a complex attenuation structure. Crust and mantle of the forearc and subducting slab are generally characterized by low attenuation (Qp > 1000). Crust and mantle beneath the magmatic arc show elevated attenuation. The strongest anomaly of extremely low Qp is found in the crust between 22° and 23°S beneath the recent volcanic arc (Qp < 100). N-S variations can be observed: The western flank of the crustal attenuation anomaly follows the curved course of the volcanic front. North of 21°S the attenuation is less developed. In the northern part of the study area the low-Qp zone penetrates in the forearc mantle down to the subducting slab. In the south a deeper zone of high attenuation is resolved between 23° and 24°S directly above the subducting slab. Low Qp in the mantle correlates with earthquake clusters. The strong crustal attenuation is confined to the distribution of young ignimbrites and silicic volcanism and is interpreted as a thermally weakened zone with partial melts. The attenuation pattern in the upper mantle might reflect the variable extent of the asthenosphere and maps variations of subduction-related hydration processes in the mantle wedge from slab-derived fluids.

  10. Health Monitoring for Airframe Structural Characterization

    NASA Technical Reports Server (NTRS)

    Munns, Thomas E.; Kent, Renee M.; Bartolini, Antony; Gause, Charles B.; Borinski, Jason W.; Dietz, Jason; Elster, Jennifer L.; Boyd, Clark; Vicari, Larry; Ray, Asok; Cooper, E. G. (Technical Monitor)

    2002-01-01

    This study established requirements for structural health monitoring systems, identified and characterized a prototype structural sensor system, developed sensor interpretation algorithms, and demonstrated the sensor systems on operationally realistic test articles. Fiber-optic corrosion sensors (i.e., moisture and metal ion sensors) and low-cycle fatigue sensors (i.e., strain and acoustic emission sensors) were evaluated to validate their suitability for monitoring aging degradation; characterize the sensor performance in aircraft environments; and demonstrate placement processes and multiplexing schemes. In addition, a unique micromachined multimeasure and sensor concept was developed and demonstrated. The results show that structural degradation of aircraft materials could be effectively detected and characterized using available and emerging sensors. A key component of the structural health monitoring capability is the ability to interpret the information provided by sensor system in order to characterize the structural condition. Novel deterministic and stochastic fatigue damage development and growth models were developed for this program. These models enable real time characterization and assessment of structural fatigue damage.

  11. A Detailed Derivation of Gaussian Orbital-Based Matrix Elements in Electron Structure Calculations

    ERIC Educational Resources Information Center

    Petersson, T.; Hellsing, B.

    2010-01-01

    A detailed derivation of analytic solutions is presented for overlap, kinetic, nuclear attraction and electron repulsion integrals involving Cartesian Gaussian-type orbitals. It is demonstrated how s-type orbitals can be used to evaluate integrals with higher angular momentum via the properties of Hermite polynomials and differentiation with…

  12. Detailed mineralogical characterization of the Bullfrog and Tram members USW-G1, with emphasis on clay mineralogy

    SciTech Connect

    Bish, D.L.

    1981-10-01

    The detailed mineralogy of the Bullfrog and Tram Members of the Crater Flat Tuff from drill hole USW-G1 has been examined, primarily to characterize fully the amounts and types of clay minerals in the tuffs and the possible effects clay minerals have on rock properties. Results of bulk sample x-ray diffraction analyses agree closely with previous determinations, although slightly higher clay mineral contents were found in this study. X-ray diffraction analysis of fine fractions revealed that the clay minerals in the tuffs are sodium-saturated montmorillonite-beidellites with typical layer charges and no high-charge layers. These smectites are found in virtually all samples of the Bullfrog and Tram, and there is no correlation between the amounts of smectites and the amounts of zeolite, quartz, and feldspar. Smectites are present in both welded and nonwelded horizons and are scarce in some zones with slight-to-absent welding.

  13. Multi-junction-solar-cell designs and characterizations based on detailed-balance principle and luminescence yields

    NASA Astrophysics Data System (ADS)

    Akiyama, Hidefumi; Zhu, Lin; Yoshita, Masahiro; Kim, Changsu; Chen, Shaoqiang; Mochizuki, Toshimitsu; Kanemitsu, Yoshihiko

    2015-03-01

    We developed a straightforward method based on detailed balance relations to analyze individual subcells in multi-junction solar cells via measuring absolute electroluminescence quantum yields. This method was applied to characterization of a InGaP/GaAs/Ge 3-junction solar cell for satellite use. In addition to subcell I-V characteristics and internal luminescence yields, we derived balance sheets of energy and carriers, which revealed respective subcell contributions of radiative and nonradiative recombination losses, junction loss, and luminescence coupling. These results provide important diagnosis and feedback to fabrications. We calculated conversion-efficiency limit and optimized bandgap energy in 2-, 3-, and 4-junction tandem solar cells, including finite values of sub-cell internal luminescence quantum yields to account for realistic material qualities in sub-cells. With reference to the measured internal luminescence quantum yields, the theoretical results provide realistic targets of efficiency limits and improved design principles of practical tandem solar cells.

  14. Obtaining detailed structural information about supramolecular systems on surfaces by combining high-resolution force microscopy with ab initio calculations.

    PubMed

    Kawai, Shigeki; Sadeghi, Ali; Xu, Feng; Feng, Xu; Peng, Lifen; Lifen, Peng; Pawlak, Rémy; Glatzel, Thilo; Willand, Alexander; Orita, Akihiro; Otera, Junzo; Goedecker, Stefan; Meyer, Ernst

    2013-10-22

    State-of-the art experimental techniques such as scanning tunneling microscopy have great difficulties in extracting detailed structural information about molecules adsorbed on surfaces. By combining atomic force microscopy and Kelvin probe force microscopy with ab initio calculations, we demonstrate that we can obtain a wealth of detailed structural information about the molecule itself and its environment. Studying an FFPB molecule on a gold surface, we are able to determine its exact location on the surface, the nature of its bonding properties with neighboring molecules that lead to the growth of one-dimensional strips, and the internal torsions and bendings of the molecule.

  15. Fluorescence microscopy for the characterization of structural integrity

    NASA Technical Reports Server (NTRS)

    Street, Kenneth W.; Leonhardt, Todd A.

    1991-01-01

    The absorption characteristics of light and the optical technique of fluorescence microscopy for enhancing metallographic interpretation are presented. Characterization of thermally sprayed coatings by optical microscopy suffers because of the tendency for misidentification of the microstructure produced by metallographic preparation. Gray scale, in bright field microscopy, is frequently the only means of differentiating the actual structural details of porosity, cracking, and debonding of coatings. Fluorescence microscopy is a technique that helps to distinguish the artifacts of metallographic preparation (pullout, cracking, debonding) from the microstructure of the specimen by color contrasting structural differences. Alternative instrumentation and the use of other dye systems are also discussed. The combination of epoxy vacuum infiltration with fluorescence microscopy to verify microstructural defects is an effective means to characterize advanced materials and to assess structural integrity.

  16. Detailed measurement of the magnitude and orientation of thermal gradients in lined boreholes for characterizing groundwater flow in fractured rock

    NASA Astrophysics Data System (ADS)

    Pehme, Peeter; Parker, Beth L.; Cherry, John A.; Blohm, Detlef

    2014-05-01

    Recent developments have led to revitalization of the use of temperature logging for characterizing flow through fractured rock. The sealing of boreholes using water-filled, flexible impermeable liners prevents vertical cross connection between fractures intersecting the hole and establishes a static water column with a temperature stratification that mimics that in the surrounding formation. Measurement of the temperature profile of the lined-hole, water column (using a high sensitivity single-point probe achieving resolution on the order of 0.001 °C) has identified fractures with active flow under ambient groundwater conditions (without cross connecting flow along the borehole). Detection of flow in fractures was further improved with the use of a heater to create thermal disequilibrium in the active line source (ALS) technique and eliminate normal depth limitations in the process. This paper presents another advancement; detailed measurement of the magnitude and direction of the thermal gradient to characterize flow through fractured rock. The temperature within the water column is measured along the length of the lined hole using a temperature vector probe (TVP): four high sensitivity sensors arranged in a tetrahedral pattern oriented using three directional magnetometers. Based on these data, the horizontal and vertical components of the thermal field, as well as the direction of temperature gradient are determined, typically at depth intervals of less than 0.01 m. This probe was assessed and refined by trials in over 30 lined boreholes; the results from two holes through a fractured dolostone aquifer in Guelph, Ontario are used as exampled. Since no other device exists for measuring flow magnitude and direction under the ambient flow condition created by lined holes, the performance of the TVP is assessed by examining the reproducibility of the temperature measurements through an ALS test, and by the consistency of the results relative to other types of

  17. Detailed simulation of structural color generation inspired by the Morpho butterfly.

    PubMed

    Steindorfer, Michael A; Schmidt, Volker; Belegratis, Maria; Stadlober, Barbara; Krenn, Joachim R

    2012-09-10

    The brilliancy and variety of structural colors found in nature has become a major scientific topic in recent years. Rapid-prototyping processes enable the fabrication of according structures, but the technical exploitation requires a profound understanding of structural features and material properties regarding the generation of reflected color. This paper presents an extensive simulation of the reflectance spectra of a simplified 2D Morpho butterfly wing model by utilizing the finite-difference time-domain method. The structural parameters are optimized for reflection in a given spectral range. A comparison to simpler models, such as a plane dielectric layer stack, provides an understanding of the origin of the reflection behavior. We find that the wavelength of the reflection maximum is mainly set by the lateral dimensions of the structures. Furthermore small variations of the vertical dimensions leave the spectral position of the reflectance wavelength unchanged, potentially reducing grating effects.

  18. Experiments In Characterizing Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Yam, Yeung; Hadaegh, Fred Y.; Bayard, David S.

    1993-01-01

    Report discusses experiments conducted to test methods of identification of vibrational and coupled rotational/vibrational modes of flexible structure. Report one in series that chronicle development of integrated system of methods, sensors, actuators, analog and digital signal-processing equipment, and algorithms to suppress vibrations in large, flexible structure even when dynamics of structure partly unknown and/or changing. Two prior articles describing aspects of research, "Autonomous Frequency-Domain Indentification" (NPO-18099), and "Automated Characterization Of Vibrations Of A Structure" (NPO-18141).

  19. Structural characterization of unusually stable polycyclic ozonides

    NASA Astrophysics Data System (ADS)

    Cusati, R. C.; Pereira, U. A.; Barbosa, L. C. A.; Maltha, C. R. A.; Carneiro, José W. M.; Corrêa, R. S.; Doriguetto, A. C.

    2015-02-01

    The single crystal structure of seven tri- and tetracyclic ozonides derived from 8-oxabicycle[3.2.1]oct-6-en-3-ones have been characterized by X-ray diffraction method. Five ozonides (4, 5, 6, 7 and 8) crystallize in the monoclinic crystal system with P21/c space group. Compound 3 crystallize in the unusual centrosymmetric space group R 3 bar m, which represents ∼0.04% of the total number of structures know. The supramolecular structure of 3 forms infinite channels in a hexagram fashion, resulting in a honeycomb-like structure. Semi-empirical (PM6) and density functional theory methods (DFT) with the B3LYP functional and the 6-31G(d) basis set were used to optimize the geometries and compute structural parameters (bond lengths, angles and dihedral angles) that could be compared to the refined crystal structure. The theoretical results show good agreements with the experimental structure.

  20. Detailed Studies on the Structure and Dynamics of Reacting Dusty Flows at Normal and Microgravity

    NASA Technical Reports Server (NTRS)

    Egolfopoulos, Fokion N.; Campbell, Charles S.

    1997-01-01

    Two-phase reacting flows are substantially less understood compared to gas phase flows. While extensive work has been done on sprays, less attention has been given to the details of dusty reacting flows. Dusty flows are of particular interest for a wide range of applications. Particles can be present in a gas intentionally or unintentionally, and they can be inert or reacting. Inert particles can be also present in an otherwise reacting gas flow, and that can lead to flame cooling and modification of the extinction limits of a combustible mixture. Reacting solid particles can release substantial amounts of heat upon oxidation, and can be used either for propulsion (e.g. Al, B, Mg) or power generation (coal). Furthermore, accidents can occur when a reacting dust accumulates in air and which, in the presence of an ignition source, can cause explosion. Such explosions can occur during lumber milling, in grain elevators, and in mine galleries.

  1. Electrochemical characterization of InP structures

    NASA Technical Reports Server (NTRS)

    Faur, Maria; Faur, Mircea; Vargas-Aburto, Carlos; Wilt, David M.; Goradia, Manju

    1992-01-01

    Electrochemical (EC) techniques represent a simple and yet accurate method to characterize InP and related materials structures. With EC techniques, uncertainties in the measurements arising from factors such as surface effects, the composition and thickness of a front dead layer, the contacts, etc., can be significantly reduced when both a suitable electrolyte is used and the measuring conditions are carefully selected. In this work, the use of photoelectrochemical techniques with InP structures is reported. The work focuses on both the characterization and the optimization of structures grown by thermal diffusion and by epitaxial methods. Characterization of the structures is done by studying the variation in the density of surface states, number of defects, and net majority carrier concentration as a function of material removed. A step-by-step optimization process of n(sup +)p and p(sup+)n InP structures is also described. This involves the passivation and subsequent removal of damaged layers in order to extract the performance parameters of solar cells fabricated with these structures.

  2. Mechanistic Details of Glutathione Biosynthesis Revealed by Crystal Structures of Saccharomyces cerevisiae Glutamate Cysteine Ligase

    SciTech Connect

    Biterova, Ekaterina I.; Barycki, Joseph J.

    2009-12-01

    Glutathione is a thiol-disulfide exchange peptide critical for buffering oxidative or chemical stress, and an essential cofactor in several biosynthesis and detoxification pathways. The rate-limiting step in its de novo biosynthesis is catalyzed by glutamate cysteine ligase, a broadly expressed enzyme for which limited structural information is available in higher eukaryotic species. Structural data are critical to the understanding of clinical glutathione deficiency, as well as rational design of enzyme modulators that could impact human disease progression. Here, we have determined the structures of Saccharomyces cerevisiae glutamate cysteine ligase (ScGCL) in the presence of glutamate and MgCl{sub 2} (2.1 {angstrom}; R = 18.2%, R{sub free} = 21.9%), and in complex with glutamate, MgCl{sub 2}, and ADP (2.7 {angstrom}; R = 19.0%, R{sub free} = 24.2%). Inspection of these structures reveals an unusual binding pocket for the {alpha}-carboxylate of the glutamate substrate and an ATP-independent Mg{sup 2+} coordination site, clarifying the Mg{sup 2+} dependence of the enzymatic reaction. The ScGCL structures were further used to generate a credible homology model of the catalytic subunit of human glutamate cysteine ligase (hGCLC). Examination of the hGCLC model suggests that post-translational modifications of cysteine residues may be involved in the regulation of enzymatic activity, and elucidates the molecular basis of glutathione deficiency associated with patient hGCLC mutations.

  3. A sedimentological approach to hydrologic characterization: A detailed three-dimensional study of an outcrop of the Sierra Ladrones Formation, Albuquerque basin

    SciTech Connect

    Lohmann, R.C.

    1992-01-01

    Three-dimensional geologic outcrop studies which quantitatively describe the geologic architecture of deposits of a specific depositional environment are a necessary requirement for characterization of the permeability structure of an aquifer. The objective of this study is to address this need for quantitative, three-dimensional outcrop studies. For this study, a 10,000 m{sup 2} by 25 m high outcrop of Pliocene-Pleistocene Sierra Ladrones Formation located near Belen, New Mexico was mapped in detail, and the geologic architecture was quantified using geostatistical variogram analysis. In general, the information contained in this study should be useful for hydrologists working on the characterization of aquifers from similar depositional environments such as this one. However, for the permeability correlation study to be truly useful, the within-element correlation structure needs to be superimposed on the elements themselves instead of using mean log (k) values, as was done for this study. Such information is derived from outcrop permeability sampling such as the work of Davis (1990) and Goggin et al. (1988).

  4. Assessment of coal-water slurry fuels for electric power generation in Southern Indiana: Part 1, Detailed resource characterization

    SciTech Connect

    Daniel, D.N.; Harvey, C.; Dazhen, T.

    1997-07-01

    Impounded coal fines, a by-product of wet coal preparation techniques, are a potential fuel resource for electric power generation due to their abundance and characteristics when burned as a coal-water slurry fuel (CWSF). Recent work by the Pennsylvania Electric Company and others has shown that co-firing CWSF composed of cleaned material from slurry impoundments can reduce emissions of nitrogen oxides by as much as twenty percent. The commercial reality of using impounded coal fines as a CWSF depends more on coal cost, processing requirements, and the value of emission reduction credits than on the quality or abundance of the material. Many Southern Indiana slurry impoundments, including those selected for characterization in this study, contain over one-million tons of fine coal. The older impoundments have a higher percentage of coarse coal. One impoundment filled prior to 1975 averages fifty percent coal particles greater than 30 mesh (600 {mu}). Improvements in preparation plant fine coal recovery circuits are reflected by an increasing percentage of less than 200 mesh (75 {mu}) coal in more recently filled impoundments. Another impoundment filled in 1995 averages forty-nine percent coal and mineral particles finer than 200 mesh. Bench scale sink/float testing showed that separating particles with a specific gravity greater than 1.7 produced a fine coal with ten percent ash and three percent sulfur. This is similar in quality, but finer in particle size, to the coal currently used in a typical coal fired power station burning typical Illinois Basin coals. Detailed characterization of two inactive impoundments highlighted the differences between coal fines in an older impoundment and one filled in the last ten years.

  5. Detailed Study of the TE band structure of two dimensional metallic photonic crystals with square symmetry

    NASA Astrophysics Data System (ADS)

    Sedghi, Aliasghar; Valiaghaie, Soma; Soufiani, Ahad Rounaghi

    2014-10-01

    By virtue of the efficiency of the Dirichlet-to-Neumann map method, we have calculated, for H-polarization (TE mode), the band structure of 2D photonic crystals with a square lattice composed of metallic rods embedded in an air background. The rod in the unit cell is chosen to be circular in shape. Here, from a practical point of view, in order to obtain maximum band gaps, we have studied the band structure as a function of the size of the rods. We have also studied the flat bands appearing in the band structures and have shown that for frequencies around the surface plasmon frequency, the modes are highly localized at the interface between the metallic rods and the air background.

  6. AFM Structural Characterization of Drinking Water Biofilm ...

    EPA Pesticide Factsheets

    Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

  7. Synthesis and structural characterization of zinc titanates

    NASA Astrophysics Data System (ADS)

    Akgül, Güvenç

    2013-04-01

    The aim of this study is to accurately obtain of local atomic structures of zinc titanates (ZnTiO3 and Zn2TiO4). Samples have been synthesized by the ball milling method using mixture of high purity ZnO and TiO2 powders. X-ray diffraction (XRD), X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) techniques have been used to probe crystal and local structures of the synthesized powders. They have been found to exhibit very high crystallinity. In addition, the EXAFS results have showed that the ball milling is a quite effective method to fabricate highly crystalline nanosized powders. The obtained results are presented in detail.

  8. Detailed characterization of the 1087 MeV/nucleon iron-56 beam used for radiobiology at the alternating gradient synchrotron

    NASA Technical Reports Server (NTRS)

    Zeitlin, C.; Heilbronn, L.; Miller, J.

    1998-01-01

    We report beam characterization and dosimetric measurements made using a 56Fe beam extracted from the Brookhaven National Laboratory Alternating Gradient Synchrotron (AGS) with a kinetic energy of 1087 MeV/nucleon. The measurements reveal that the depth-dose distribution of this beam differs significantly from that obtained with a 600 MeV/nucleon iron beam used in several earlier radiobiology experiments at the Lawrence Berkeley National Laboratory's BEVALAC. We present detailed measurements of beam parameters relevant for radiobiology, including track- and dose-averaged linear energy transfer (LET), fragment composition and LET spectra measured behind sample holders used in irradiations of biological samples. We also report measurements of fluence behind three depths (1.94, 4.68 and 9.35 g cm(-2)) of polyethylene targets with the 1087 MeV/nucleon beam, and behind 1.94 g cm(-2) of polyethylene with a 610 MeV/nucleon beam delivered by the AGS. These results are compared to earlier measurements with the 600 MeV/nucleon beam at the BEVALAC.

  9. The effects of design details on cost and weight of fuselage structures

    NASA Technical Reports Server (NTRS)

    Swanson, G. D.; Metschan, S. L.; Morris, M. R.; Kassapoglou, C.

    1993-01-01

    Crown panel design studies showing the relationship between panel size, cost, weight, and aircraft configuration are compared to aluminum design configurations. The effects of a stiffened sandwich design concept are also discussed. This paper summarizes the effect of a design cost model in assessing the cost and weight relationships for fuselage crown panel designs. Studies were performed using data from existing aircraft to assess the effects of different design variables on the cost and weight of transport fuselage crown panel design. Results show a strong influence of load levels, panel size, and material choices on the cost and weight of specific designs. A design tool being developed under the NASA ACT program is used in the study to assess these issues. The effects of panel configuration comparing postbuckled and buckle resistant stiffened laminated structure is compared to a stiffened sandwich concept. Results suggest some potential economy with stiffened sandwich designs for compression dominated structure with relatively high load levels.

  10. Detailed Study of Emission Structures in the Vicinity of LkHα 198

    NASA Astrophysics Data System (ADS)

    Gevorgyan, M. H.; Movsessian, T. A.; Andreasyan, H. R.; Magakian, T. Yu.

    2016-09-01

    Results from a study of collimated flows near the star LkHα 198 are reported. Observations were made using the VAGR multipupil spectrograph installed on the 2.6-m telescope at the Byurakan Astrophysical Observatory. The morphology and kinematics of emission structures in the vicinity of LkHα 198, including HH 161, were studied and electron density charts obtained. Besides the HH 161 object, our data revealed an arc-shaped emission structure with LkHα 198 at its apex. A shape of this kind is usually a direct indication of the presence of a cavity in a dark cloud blown out by a directed outflow. In addition, a faint "tail" extending in the direction of the central star is observed in HH 161. A comparison of these results with radio frequency observations shows that the probable source of HH 161 is the binary system LkHα 198.

  11. A detailed view of a ribosomal active site: the structure of the L11-RNA complex.

    PubMed

    Wimberly, B T; Guymon, R; McCutcheon, J P; White, S W; Ramakrishnan, V

    1999-05-14

    We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. The highly compact RNA has both familiar and novel structural motifs. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors.

  12. The detailed spatial structure of field-aligned currents comprising the substorm current wedge

    NASA Astrophysics Data System (ADS)

    Murphy, Kyle R.; Mann, Ian R.; Rae, I. Jonathan; Waters, Colin L.; Frey, Harald U.; Kale, Andy; Singer, Howard J.; Anderson, Brian J.; Korth, Haje

    2013-12-01

    We present a comprehensive two-dimensional view of the field-aligned currents (FACs) during the late growth and expansion phases for three isolated substorms utilizing in situ observations from the Active Magnetosphere and Planetary Electrodynamics Response Experiment and from ground-based magnetometer and optical instrumentation from the Canadian Array for Realtime Investigations of Magnetic Activity and Time History of Events and Macroscale Interactions during Substorms ground-based arrays. We demonstrate that the structure of FACs formed during the expansion phase and associated with the substorm current wedge is significantly more complex than a simple equivalent line current model comprising a downward FAC in the east and upward FAC in the west. This two-dimensional view demonstrates that azimuthal bands of upward and downward FACs with periodic structuring in latitude form across midnight and can span up to 8 h of magnetic local time. However, when averaged over latitude, the overall longitudinal structure of the net FACs resembles the simpler equivalent line current description of the substorm current wedge (SCW). In addition, we demonstrate that the upward FAC elements of the structured SCW are spatially very well correlated with discrete aurora during the substorm expansion phase and that discrete changes in the FAC topology are observed in the late growth phase prior to auroral substorm expansion phase onset. These observations have important implications for determining how the magnetosphere and ionosphere couple during the late growth phase and expansion phase, as well as providing important constraints on the magnetospheric generator of the FACs comprising the SCW.

  13. Detailed Post-Soft Impact Progressive Damage Assessment for Hybrid Structure Jet Engines

    NASA Technical Reports Server (NTRS)

    Siddens, Aaron; Bayandor, Javid; Celestina, Mark L.

    2014-01-01

    Currently, certification of engine designs for resistance to bird strike is reliant on physical tests. Predictive modeling of engine structural damage has mostly been limited to evaluation of individual forward section components, such as fan blades within a fixed frame of reference, to direct impact with a bird. Such models must be extended to include interactions among engine components under operating conditions to evaluate the full extent of engine damage. This paper presents the results of a study aim to develop a methodology for evaluating bird strike damage in advanced propulsion systems incorporating hybrid composite/metal structures. The initial degradation and failure of individual fan blades struck by a bird were investigated. Subsequent damage to other fan blades and engine components due to resultant violent fan assembly vibrations and fragmentation was further evaluated. Various modeling parameters for the bird and engine components were investigated to determine guidelines for accurately capturing initial damage and progressive failure of engine components. Then, a novel hybrid structure modeling approach was investigated and incorporated into the crashworthiness methodology. Such a tool is invaluable to the process of design, development, and certification of future advanced propulsion systems.

  14. Crystal structure of α5β1 integrin ectodomain: Atomic details of the fibronectin receptor

    PubMed Central

    Nagae, Masamichi; Re, Suyong; Mihara, Emiko; Nogi, Terukazu; Sugita, Yuji

    2012-01-01

    Integrin α5β1 is a major cellular receptor for the extracellular matrix protein fibronectin and plays a fundamental role during mammalian development. A crystal structure of the α5β1 integrin headpiece fragment bound by an allosteric inhibitory antibody was determined at a 2.9-Å resolution both in the absence and presence of a ligand peptide containing the Arg-Gly-Asp (RGD) sequence. The antibody-bound β1 chain accommodated the RGD ligand with very limited structural changes, which may represent the initial step of cell adhesion mediated by nonactivated integrins. Furthermore, a molecular dynamics simulation pointed to an important role for Ca2+ in the conformational coupling between the ligand-binding site and the rest of the molecule. The RGD-binding pocket is situated at the center of a trenchlike exposed surface on the top face of α5β1 devoid of glycosylation sites. The structure also enabled the precise prediction of the acceptor residue for the auxiliary synergy site of fibronectin on the α5 subunit, which was experimentally confirmed by mutagenesis and kinetic binding assays. PMID:22451694

  15. The structure of apo human glutamate dehydrogenase details subunit communication and allostery.

    PubMed

    Smith, Thomas J; Schmidt, Timothy; Fang, Jie; Wu, Jane; Siuzdak, Gary; Stanley, Charles A

    2002-05-03

    The structure of human glutamate dehydrogenase (GDH) has been determined in the absence of active site and regulatory ligands. Compared to the structures of bovine GDH that were complexed with coenzyme and substrate, the NAD binding domain is rotated away from the glutamate-binding domain. The electron density of this domain is more disordered the further it is from the pivot helix. Mass spectrometry results suggest that this is likely due to the apo form being more dynamic than the closed form. The antenna undergoes significant conformational changes as the catalytic cleft opens. The ascending helix in the antenna moves in a clockwise manner and the helix in the descending strand contracts in a manner akin to the relaxation of an extended spring. A number of spontaneous mutations in this antenna region cause the hyperinsulinism/hyperammonemia syndrome by decreasing GDH sensitivity to the inhibitor, GTP. Since these residues do not directly contact the bound GTP, the conformational changes in the antenna are apparently crucial to GTP inhibition. In the open conformation, the GTP binding site is distorted such that it can no longer bind GTP. In contrast, ADP binding benefits by the opening of the catalytic cleft since R463 on the pivot helix is pushed into contact distance with the beta-phosphate of ADP. These results support the previous proposal that purines regulate GDH activity by altering the dynamics of the NAD binding domain. Finally, a possible structural mechanism for negative cooperativity is presented.

  16. A detailed study of nucleon structure function in nuclei in the valence quark region

    SciTech Connect

    Bianchi, N.

    1994-04-01

    The so called {open_quotes}EMC effect{close_quotes} discovered during the 1980`s, has caused a big controversy in the community of nuclear and high energy physicists; during the last ten years, five experiments have been performed in different laboratories and several hundreds of papers about the possible interpretation of the modification of the nucleon structure function inside nuclei have been published. However, from the experimental point of view, the main goal of four experiments (EMC, BCDMS, NMC, FNAL) has been to emphasize the region of low x{sub b}, where shadowing effects appear. In the region of valence quarks and nuclear effects (x{sub b} > 0.1 - 0.2) the most reliable data presently available are from the SLAC E139 experiment performed in 1983 with only 80 hours of beam time. New precise data in the valence quark region are necessary to measure separate structure functions F{sub 2}(x{sub b}, Q{sup 2}) and R{sup lt}(x{sub b},Q{sup 2}) = {sigma}{sub l}/{sigma}{sub t}, and to investigate the real A-dependence of the ratio between bound and free-nucleon structure functions which is not completely defined by the SLAC data. Moreover, from the nuclear physics point of view, a measurement on some unexplored nuclei, like {sup 3}He and {sup 48}Ca, would be of great interest. The intermediate scaling region (0.1 < x{sub b} < 0.7) would be accessible at CEBAF if the machine energy will reach 6-8 GeV, as suggested by all the tests performed on the RF cavities. This physics program has been already presented in two letter of intents.

  17. Structural details of the Orion Nebula - Detection of a network of stringlike ionized features

    NASA Astrophysics Data System (ADS)

    Yusef-Zadeh, F.

    1990-09-01

    Continuum observations of the Orion Nebula, obtained at 20 cm using the A, B, C, and D configurations of the VLA during 1986-1987, are reported. Radio images of resolution 1.8 x 1.6 arcsec are presented and analyzed, with a focus on (1) the complex cone structure of M 42 and (2) an extended network of bright stringlike features concentrated near the Trapezium cluster. Possible theoretical explanations of these features are explored, starting from the blister model of H II regions developed by Tenorio and Tagle (1979).

  18. Coupling geostatistics to detailed reservoir description allows better visualization and more accurate characterization/simulation of turbidite reservoirs: Elk Hills oil field, California

    SciTech Connect

    Allan, M.E.; Wilson, M.L.; Wightman, J. )

    1996-01-01

    The Elk Hills giant oilfield, located in the southern San Joaquin Valley of California, has produced 1.1 billion barrels of oil from Miocene and shallow Pliocene reservoirs. 65% of the current 64,000 BOPD production is from the pressure-supported, deeper Miocene turbidite sands. In the turbidite sands of the 31 S structure, large porosity permeability variations in the Main Body B and Western 31 S sands cause problems with the efficiency of the waterflooding. These variations have now been quantified and visualized using geostatistics. The end result is a more detailed reservoir characterization for simulation. Traditional reservoir descriptions based on marker correlations, cross-sections and mapping do not provide enough detail to capture the short-scale stratigraphic heterogeneity needed for adequate reservoir simulation. These deterministic descriptions are inadequate to tie with production data as the thinly bedded sand/shale sequences blur into a falsely homogenous picture. By studying the variability of the geologic petrophysical data vertically within each wellbore and spatially from well to well, a geostatistical reservoir description has been developed. It captures the natural variability of the sands and shales that was lacking from earlier work. These geostatistical studies allow the geologic and petrophysical characteristics to be considered in a probabilistic model. The end-product is a reservoir description that captures the variability of the reservoir sequences and can be used as a more realistic starting point for history matching and reservoir simulation.

  19. Coupling geostatistics to detailed reservoir description allows better visualization and more accurate characterization/simulation of turbidite reservoirs: Elk Hills oil field, California

    SciTech Connect

    Allan, M.E.; Wilson, M.L.; Wightman, J.

    1996-12-31

    The Elk Hills giant oilfield, located in the southern San Joaquin Valley of California, has produced 1.1 billion barrels of oil from Miocene and shallow Pliocene reservoirs. 65% of the current 64,000 BOPD production is from the pressure-supported, deeper Miocene turbidite sands. In the turbidite sands of the 31 S structure, large porosity & permeability variations in the Main Body B and Western 31 S sands cause problems with the efficiency of the waterflooding. These variations have now been quantified and visualized using geostatistics. The end result is a more detailed reservoir characterization for simulation. Traditional reservoir descriptions based on marker correlations, cross-sections and mapping do not provide enough detail to capture the short-scale stratigraphic heterogeneity needed for adequate reservoir simulation. These deterministic descriptions are inadequate to tie with production data as the thinly bedded sand/shale sequences blur into a falsely homogenous picture. By studying the variability of the geologic & petrophysical data vertically within each wellbore and spatially from well to well, a geostatistical reservoir description has been developed. It captures the natural variability of the sands and shales that was lacking from earlier work. These geostatistical studies allow the geologic and petrophysical characteristics to be considered in a probabilistic model. The end-product is a reservoir description that captures the variability of the reservoir sequences and can be used as a more realistic starting point for history matching and reservoir simulation.

  20. Detailed design of a lattice composite fuselage structure by a mixed optimization method

    NASA Astrophysics Data System (ADS)

    Liu, D.; Lohse-Busch, H.; Toropov, V.; Hühne, C.; Armani, U.

    2016-10-01

    In this article, a procedure for designing a lattice fuselage barrel is developed. It comprises three stages: first, topology optimization of an aircraft fuselage barrel is performed with respect to weight and structural performance to obtain the conceptual design. The interpretation of the optimal result is given to demonstrate the development of this new lattice airframe concept for the fuselage barrel. Subsequently, parametric optimization of the lattice aircraft fuselage barrel is carried out using genetic algorithms on metamodels generated with genetic programming from a 101-point optimal Latin hypercube design of experiments. The optimal design is achieved in terms of weight savings subject to stability, global stiffness and strain requirements, and then verified by the fine mesh finite element simulation of the lattice fuselage barrel. Finally, a practical design of the composite skin complying with the aircraft industry lay-up rules is presented. It is concluded that the mixed optimization method, combining topology optimization with the global metamodel-based approach, allows the problem to be solved with sufficient accuracy and provides the designers with a wealth of information on the structural behaviour of the novel anisogrid composite fuselage design.

  1. Accuracy assessment of modeling architectural structures and details using terrestrial laser scanning

    NASA Astrophysics Data System (ADS)

    Kedzierski, M.; Walczykowski, P.; Orych, A.; Czarnecka, P.

    2015-08-01

    One of the most important aspects when performing architectural documentation of cultural heritage structures is the accuracy of both the data and the products which are generated from these data: documentation in the form of 3D models or vector drawings. The paper describes an assessment of the accuracy of modelling data acquired using a terrestrial phase scanner in relation to the density of a point cloud representing the surface of different types of construction materials typical for cultural heritage structures. This analysis includes the impact of the scanning geometry: the incidence angle of the laser beam and the scanning distance. For the purposes of this research, a test field consisting of samples of different types of construction materials (brick, wood, plastic, plaster, a ceramic tile, sheet metal) was built. The study involved conducting measurements at different angles and from a range of distances for chosen scanning densities. Data, acquired in the form of point clouds, were then filtered and modelled. An accuracy assessment of the 3D model was conducted by fitting it with the point cloud. The reflection intensity of each type of material was also analyzed, trying to determine which construction materials have the highest reflectance coefficients, and which have the lowest reflection coefficients, and in turn how this variable changes for different scanning parameters. Additionally measurements were taken of a fragment of a building in order to compare the results obtained in laboratory conditions, with those taken in field conditions.

  2. A detailed three-dimensional P-wave velocity structure in Italy from local earthquake tomography

    NASA Astrophysics Data System (ADS)

    di Stefano, Raffaele; Castello, Barbara; Chiarabba, Claudio; Grazia Ciaccio, Maria

    2010-05-01

    We here present an updated high resolution tomographic P-wave velocity model of the lithosphere in Italy, obtained by adding about 296,600 P-wave arrival observations from ~7.200 earthquakes, from the preliminary update of the CSI 2.0, recorded in the period 2003-2007, to the previously inverted dataset (165,000 P-wave arrivals).Additional events have been strictly selected for location quality (azimuthal gap < 135°; horizontal error <= 2km; vertical error <= 4km; rms < 1s) and a number of P-wave observations >= 8. Our results confirm the main structural features in the best resolved parts of the inverted volume and show a much better resolution in some of the previously less resolved areas, due to both the larger number of inverted phases and the more even distribution of seismic stations. Surface basins and relationships between the Adriatic, Tyrrhenian, and European plates are better imaged. The integrated analysis of 20 years of seismicity and the high resolution tomographic images obtained, allows us to add new constraints to the kynematics and the geodynamics of the lithosphere-asthenosphere system in this region. We also present preliminary results obtained by thickening the nodes spacing from 15km x15km to 10km x 10km and we finally compare the complex velocity structures imaged by the inversion of the two different grid spacing.

  3. Unveiling details of defect structures in chiral and achiral nematic droplets by improving simulations of optical images

    NASA Astrophysics Data System (ADS)

    Mur, Urban; Čopar, Simon; Ravnik, Miha; Čančula, Miha; Žumer, Slobodan

    2016-09-01

    There is a great increase of interest in the nematic defect structures, where interplay of confinement, elasticity, anchoring, and chirality leads to complex ordering fields with singular topological defects and nonsingular solitonic deformations. Beside numerous advanced microscopy techniques, the standard polarized optical microscopy is still an elementary first-to-take tool in use. To fully capture its potential and understand the limitations in unveiling the details of complex structures, we apply a recently extended Jones matrix approach based on ray-tracing that allows to include also effects of focusing and numerical aperture. The approach is illustrated with results of recent studies of cholesteric droplets.

  4. Detailed Analysis of the Structural Changes of Bone Matrix During the Demineralization Process Using Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Timchenko, E. V.; Zherdeva, L. A.; Timchenko, P. E.; Volova, L. T.; Ponomareva, U. V.

    The results of experimental research of human cortical bone tissue depending on demineralization time were represented using Raman spectroscopy. Depending on demineralization time the ratio of the mineral (РO43- and CO32-) and organic components (amide I) of bone tissue, as well as changes in the spectral regions responsible for the structural integrity of the collagen fibers in bone tissue (1200-1460 cm-1 and 2880-3000 cm-1) were investigated. The observed changes show a decrease in mineral components: thus, the value of Raman band intensity at 956 and 1069 cm-1 for 5 minutes demineralization is 68.5 and 77.3%, for 20 minutes - 55.1 and 61.1%, for 120 minutes - 32.8 and 37% from Raman intensity values of not demineralized tissue objects respectively.

  5. Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

    PubMed

    Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

    2014-04-28

    Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

  6. Systematic Survey of Clonal Complexity in Tuberculosis at a Populational Level and Detailed Characterization of the Isolates Involved ▿

    PubMed Central

    Navarro, Yurena; Herranz, Marta; Pérez-Lago, Laura; Martínez Lirola, Miguel; Ruiz-Serrano, Maria Jesús; Bouza, Emilio; García de Viedma, Darío

    2011-01-01

    Clonally complex infections by Mycobacterium tuberculosis are progressively more accepted. Studies of their dimension in epidemiological scenarios where the infective pressure is not high are scarce. Our study systematically searched for clonally complex infections (mixed infections by more than one strain and simultaneous presence of clonal variants) by applying mycobacterial interspersed repetitive-unit (MIRU)–variable-number tandem-repeat (VNTR) analysis to M. tuberculosis isolates from two population-based samples of respiratory (703 cases) and respiratory-extrapulmonary (R+E) tuberculosis (TB) cases (71 cases) in a context of moderate TB incidence. Clonally complex infections were found in 11 (1.6%) of the respiratory TB cases and in 10 (14.1%) of those with R+E TB. Among the 21 cases with clonally complex TB, 9 were infected by 2 independent strains and the remaining 12 showed the simultaneous presence of 2 to 3 clonal variants. For the 10 R+E TB cases with clonally complex infections, compartmentalization (different compositions of strains/clonal variants in independent infected sites) was found in 9 of them. All the strains/clonal variants were also genotyped by IS6110-based restriction fragment length polymorphism analysis, which split two MIRU-defined clonal variants, although in general, it showed a lower discriminatory power to identify the clonal heterogeneity revealed by MIRU-VNTR analysis. The comparative analysis of IS6110 insertion sites between coinfecting clonal variants showed differences in the genes coding for a cutinase, a PPE family protein, and two conserved hypothetical proteins. Diagnostic delay, existence of previous TB, risk for overexposure, and clustered/orphan status of the involved strains were analyzed to propose possible explanations for the cases with clonally complex infections. Our study characterizes in detail all the clonally complex infections by M. tuberculosis found in a systematic survey and contributes to the

  7. Detailed compositional characterization of plastic waste pyrolysis oil by comprehensive two-dimensional gas-chromatography coupled to multiple detectors.

    PubMed

    Toraman, Hilal E; Dijkmans, Thomas; Djokic, Marko R; Van Geem, Kevin M; Marin, Guy B

    2014-09-12

    The detailed compositional characterization of plastic waste pyrolysis oil was performed with comprehensive two-dimensional GC (GC×GC) coupled to four different detectors: a flame ionization detector (FID), a sulfur chemiluminescence detector (SCD), a nitrogen chemiluminescence detector (NCD) and a time of flight mass spectrometer (TOF-MS). The performances of different column combinations were assessed in normal i.e. apolar/mid-polar and reversed configurations for the GC×GC-NCD and GC×GC-SCD analyses. The information obtained from the four detectors and the use of internal standards, i.e. 3-chlorothiophene for the FID and the SCD and 2-chloropyridine for the NCD analysis, enabled the identification and quantification of the pyrolysis oil in terms of both group type and carbon number: hydrocarbon groups (n-paraffins, iso-paraffins, olefins and naphthenes, monoaromatics, naphthenoaromatics, diaromatics, naphthenodiaromatics, triaromatics, naphthenotriaromatics and tetra-aromatics), nitrogen (nitriles, pyridines, quinolines, indole, caprolactam, etc.), sulfur (thiols/sulfides, thiophenes/disulfides, benzothiophenes, dibenzothiophenes, etc.) and oxygen containing compounds (ketones, phenols, aldehydes, ethers, etc.). Quantification of trace impurities is illustrated for indole and caprolactam. The analyzed pyrolysis oil included a significant amount of nitrogen containing compounds (6.4wt%) and to a lesser extent sulfur containing compounds (0.6wt%). These nitrogen and sulfur containing compounds described approximately 80% of the total peak volume for respectively the NCD and SCD analysis. TOF-MS indicated the presence of the oxygen containing compounds. However only a part of the oxygen containing compounds (2.5wt%) was identified because of their low concentrations and possible overlap with the complex hydrocarbon matrix as no selective detector or preparative separation for oxygen compounds was used.

  8. Detailed characterization of mechanical properties and molecular mobility within dry seed glasses: relevance to the physiology of dry biological systems.

    PubMed

    Ballesteros, Daniel; Walters, Christina

    2011-11-01

    Slow movement of molecules in glassy matrices controls the kinetics of chemical and physical reactions in dry seeds. Variation in physiological activity among seeds suggests that there are differences in mobility among seed glasses. Testing this hypothesis is difficult because few tools are available to measure molecular mobility within dry seeds. Here, motional properties within dry pea cotyledons were assessed using dynamic mechanical analysis. The technique detected several molecular relaxations between -80 and +80°C and gave a more detailed description of water content-temperature effects on molecular motion than previously understood from studies of glass formation in seeds at glass transition (Tg). Diffusive movement is delimited by the α relaxation, which appears to be analogous to Tg. β and γ relaxations were also detected at temperatures lower than α relaxations, clearly demonstrating intramolecular motion within the glassy matrix of the pea cotyledon. Glass transitions, or the mechanical counterpart α relaxation, appear to be less relevant to seed aging during dry storage than previously thought. On the other hand, β relaxation occurs at temperature and moisture conditions typically used for seed storage and has established importance for physical aging of synthetic polymer glasses. Our data show that the nature and extent of molecular motion varies considerably with moisture and temperature, and that the hydrated conditions used for accelerated aging experiments and ultra-dry conditions sometimes recommended for seed storage give greater molecular mobility than more standard seed storage practices. We believe characterization of molecular mobility is critical for evaluating how dry seeds respond to the environment and persist through time.

  9. Detailed Structure of the Outer Disk Around HD 169142 with Polarized Light in H-band

    NASA Technical Reports Server (NTRS)

    Momose, Munetake; Morita, Ayaka; Fukagawa, Misato; Muto, Takayuki; Takeuchi, Taku; Hashimoto, Jun; Honda, Mitsuhiko; Kudo, Tomoyuki; Okamoto, Yoshiko K.; Kanagawa, Kazuhiro D.; Tanaka, Hidekazu; Grady, Carol A.; Sitko, Michael L.; Akiyama, Eiji; Currie, Thayne; Follette, Katherine B.; Mayama, Satoshi; Kusakabe, Nobuhiko; Abe, Lyu; Brandner, Wolfgang; Brandt, Timothy D.; Carson, Joseph C.; Egner, Sebastian; Feldt, Markus; McElwain, Michael W.

    2015-01-01

    Coronagraphic imagery of the circumstellar disk around HD 169142 in H-band polarized intensity (PI) with Subaru/HiCIAO is presented. The emission scattered by dust particles at the disk surface in 0.''2=r=1.''2, or 29=r=174 AU, is successfully detected. The azimuthally-averaged radial profile of the PI shows a double power-law distribution, in which the PIs in r = 29-52 AU and r = 81.2-145 AU respectively show r-3-dependence. These two power-law regions are connected smoothly with a transition zone (TZ), exhibiting an apparent gap in r = 40-70 AU. The PI in the inner power-law region shows a deep minimum whose location seems to coincide with the point source at lambda = 7 mm. This can be regarded as another sign of a protoplanet in TZ. The observed radial profile of the PI is reproduced by a minimally flaring disk with an irregular surface density distribution or with an irregular temperature distribution or with the combination of both. The depletion factor of surface density in the inner power-law region (r <50 AU) is derived to be =0.16 from a simple model calculation. The obtained PI image also shows small scale asymmetries in the outer power-law region. Possible origins for these asymmetries include corrugation of the scattering surface in the outer region, and shadowing effect by a puffed up structure in the inner power-law region.

  10. A detailed structural comparison between the charge relay system in chymotrypsinogen and in alpha-chymotrypsin.

    PubMed

    Birktoft, J J; Kraut, J; Freer, S T

    1976-10-05

    An improved 2.5-A electron density map of chymotrypsinogen was calculated by incorporating heavy-atom anomalous scattering effects and a new model of the molecule was constructed. Phases from x-ray structure factors (R = 0.43) computed from this model were then used in the calculation of another electron density map against which the model was further refined. The catalytic Ser-195 side chain in the new model is in the "down" or "acyl" orientation and its Ogamma atom is in position to form a normal hydrogen bond with Nepsilon2 of His-57. In contrast, the corresponding hydrogen bond in alpha-chymotrypsin (Birktoft, J.J., and Blow, D.M. (1972), J.Mol. Biol. 68, 187) is severely distorted, probably as a consequence of a 1.5-A shift in the relative positions of the two cylindrical folding domains composing most of the molecule. We suggest that this activiation induced distortion of the charge-relay, hydrogen-bonding system plays an important role in the genesis of enzymic activity, in accord with an earlier proposal by Wang concerning the role of bent hydrogen bonds in enzyme catalysis (Wang, J.J. (1970), Proc. Natl. Acad. Sci. U.S.A. 66, 874).

  11. Conjugation of α-amylase with dextran for enhanced stability: process details, kinetics and structural analysis.

    PubMed

    Jadhav, Swati B; Singhal, Rekha S

    2012-11-06

    The influence of enzyme polysaccharide interaction on enzyme stability and activity was elucidated by covalently binding dextran to a model enzyme, α-amylase. The conjugation process was optimized with respect to concentration of oxidizing agent, pH of enzyme solution, ratio of dextran to enzyme concentration, temperature and time of conjugate formation, and was found to affect the stability of α-amylase. α-Amylase conjugated under optimized conditions showed 5% loss of activity but with enhanced thermal and pH stability. Lower inactivation rate constant of conjugated α-amylase within the temperature range of 60-80 °C implied its better stability. Activation energy for denaturation of α-amylase increased by 8.81 kJ/mol on conjugation with dextran. Analysis of secondary structure of α-amylase after covalent binding with dextran showed helix to turn conversion without loss of functional properties of α-amylase. Covalent bonding was found to be mandatory for the formation of conjugate.

  12. Characterization and Cure Monitoring of Structural Adhesives

    DTIC Science & Technology

    1989-02-01

    OX tiLE (OP? MTL TR 89-15 AD CHARACTERIZATION AND CURE MONITORING OF STRUCTURAL ADHESIVES CD WALTER X. ZUKAS, HOWARD H. WONG, DAVID A. DUNN, and...REPORT NUMB3ER 7. AUTHOR(s) 8. CONTRACT OR GRANT NUMBERs) Walter X. Zukas, Howard H. Wong, David A. Dunn, and Stanley E. Wentworth I. PERFORING...Technology, Gaithersburg, MD 20899 1 ATTN: B. Fanconi, Polymer Standards Division 1 D. Hunston, Polymer Standards Division 1 Dr. Stanley M. Barkin , Staff

  13. Herschel far-infrared observations of the Carina Nebula complex. III. Detailed cloud structure and feedback effects

    NASA Astrophysics Data System (ADS)

    Roccatagliata, V.; Preibisch, T.; Ratzka, T.; Gaczkowski, B.

    2013-06-01

    Context. The star formation process in large clusters/associations can be strongly influenced by the feedback from high-mass stars. Whether the resulting net effect of the feedback is predominantly negative (cloud dispersal) or positive (triggering of star formation due to cloud compression) is still an open question. Aims: The Carina Nebula complex (CNC) represents one of the most massive star-forming regions in our Galaxy. We use our Herschel far-infrared observations to study the properties of the clouds over the entire area of the CNC (with a diameter of ≈3.2°, which corresponds to ≈125 pc at a distance of 2.3 kpc). The good angular resolution (10''-36'') of the Herschel maps corresponds to physical scales of 0.1-0.4 pc, and allows us to analyze the small-scale (i.e., clump-size) structures of the clouds. Methods: The full extent of the CNC was mapped with PACS and SPIRE in the 70, 160, 250, 350, and 500 μm bands. We determined temperatures and column densities at each point in these maps by modeling the observed far-infrared spectral energy distributions. We also derived a map showing the strength of the UV radiation field. We investigated the relation between the cloud properties and the spatial distribution of the high-mass stars and computed total cloud masses for different density thresholds. Results: Our Herschel maps resolve for the first time the small-scale structure of the dense clouds over the entire spatial extent of the CNC. Several particularly interesting regions, including the prominent pillars south of η Car, are analyzed in detail. We compare the cloud masses derived from the Herschel data with previous mass estimates based on sub-mm and molecular line data. Our maps also reveal a peculiar wave-like pattern in the northern part of the Carina Nebula. Finally, we characterize two prominent cloud complexes at the periphery of our Herschel maps, which are probably molecular clouds in the Galactic background. Conclusions: We find that the

  14. Calculation of stellar structure. IV. Results using a detailed energy generation subroutine.

    NASA Astrophysics Data System (ADS)

    Rouse, C. A.

    1995-12-01

    The results from two solar model calculations using the "energy.for" energy generation and neutrino flux code (Bahcall & Pinsonneault 1992) are presented. The models of the present Sun were generated using the program described in the first three papers of this series and using only the helium abundance profile from the Bahcall & Ulrich (1988) (BU) standard model in the present model structure calculations. One model is a simulation of the BU model and yields a ^37^Cl solar neutrino counting rate of 7.0SNU (compared to 7.9SNU for the BU model) and a ^71^Ga neutrino experiment counting rate between 112 and 137SNU (compared to 132SNU for the BU model). The second model has a postulated small high-Z core (Rouse 1983) and yields a ^37^Cl neutrino experiment counting rate of 2.45SNU that is within one sigma of the Homestake Collaboration observed rate of (2.55+/-0.25)SNU (see Parke 1995). It yields a ^71^Ga neutrino experiment counting rate between 89 and 103SNU that is within one sigma of the GALLEX Collaboration neutrino experiment observed rate of (79+/-12)SNU (see Parke 1995). The theoretical ^8^B solar neutrino flux and the observed Kamiokande ^8^B flux (Hirata et al. 1989) are discussed regarding the puzzle of explaining both the chlorine experiment results and the Kamiokande results. The modification of the energy.for code for use in the current Rouse program is described. Consistency of a high-Z core solar model with theories of star formation from pre-stellar nuclei (Krat 1952; Urey 1956; Huang 1957) is suggested.

  15. Detailed structure of the outer disk around HD 169142 with polarized light in H-band

    NASA Astrophysics Data System (ADS)

    Momose, Munetake; Morita, Ayaka; Fukagawa, Misato; Muto, Takayuki; Takeuchi, Taku; Hashimoto, Jun; Honda, Mitsuhiko; Kudo, Tomoyuki; Okamoto, Yoshiko K.; Kanagawa, Kazuhiro D.; Tanaka, Hidekazu; Grady, Carol A.; Sitko, Michael L.; Akiyama, Eiji; Currie, Thayne; Follette, Katherine B.; Mayama, Satoshi; Kusakabe, Nobuhiko; Abe, Lyu; Brandner, Wolfgang; Brandt, Timothy D.; Carson, Joseph C.; Egner, Sebastian; Feldt, Markus; Goto, Miwa; Guyon, Olivier; Hayano, Yutaka; Hayashi, Masahiko; Hayashi, Saeko S.; Henning, Thomas; Hodapp, Klaus W.; Ishii, Miki; Iye, Masanori; Janson, Markus; Kandori, Ryo; Knapp, Gillian R.; Kuzuhara, Masayuki; Kwon, Jungmi; Matsuo, Taro; McElwain, Michael W.; Miyama, Shoken; Morino, Jun-Ichi; Moro-Martin, Amaya; Nishimura, Tetsuo; Pyo, Tae-Soo; Serabyn, Eugene; Suenaga, Takuya; Suto, Hiroshi; Suzuki, Ryuji; Takahashi, Yasuhiro H.; Takami, Michihiro; Takato, Naruhisa; Terada, Hiroshi; Thalmann, Christian; Tomono, Daigo; Turner, Edwin L.; Watanabe, Makoto; Wisniewski, John; Yamada, Toru; Takami, Hideki; Usuda, Tomonori; Tamura, Motohide

    2015-10-01

    Coronagraphic imagery of the circumstellar disk around HD 169142 in H-band polarized intensity (PI) with Subaru/HiCIAO is presented. The emission scattered by dust particles at the disk surface in 0{^''.}2 ≤ r ≤ 1{^''.}2, or 29 ≤ r ≤ 174 au, is successfully detected. The azimuthally averaged radial profile of the PI shows a double power-law distribution, in which the PIs in r = 29-52 au and r = 81.2-145 au respectively show r-3 dependence. These two power-law regions are connected smoothly with a transition zone (TZ), exhibiting an apparent gap in r = 40-70 au. The PI in the inner power-law region shows a deep minimum whose location seems to coincide with the point source at λ = 7 mm. This can be regarded as another sign of a protoplanet in the TZ. The observed radial profile of the PI is reproduced by a minimally flaring disk with an irregular surface density distribution, an irregular temperature distribution, or with a combination of both. The depletion factor of surface density in the inner power-law region (r < 50 au) is derived to be ≥ 0.16 from a simple model calculation. The obtained PI image also shows small-scale asymmetries in the outer power-law region. Possible origins for these asymmetries include corrugation of the scattering surface in the outer region, and a shadowing effect by a puffed-up structure in the inner power-law region.

  16. Detailed studies on substrate structure requirements of glycoamidases A and F.

    PubMed

    Fan, J Q; Lee, Y C

    1997-10-24

    Glycoamidases (peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase, EC 3.5.1.52; also known as peptide: N-glycanases (PNGases) release N-linked oligosaccharides from glycopeptides and/or glycoproteins by hydrolyzing the glycosylated beta-amide bond of the asparagine side chain. The most widely used glycoamidases are those from Flavobacterium meningosepticum (glycoamidase F or PNGase F) and almond emulsin (glycoamidase A or PNGase A). To study the substrate structure requirement of these enzymes systematically, we synthesized >30 glycopeptides containing cellobiose, lactose, GlcNAc, and di-N,N'-acetylchitobiose (CTB). The length of the peptide was varied from one to five amino acids, and glycosylamines were linked to either Asn or Gln located at different positions in the peptide, including NH2 and COOH termini. Neither enzyme could cleave cellobiose and lactose glycopeptides, indicating that the 2-acetamido group on the Asn-linked GlcNAc is important in the recognition by both glycoamidases A and F. GlcNAc peptides could be cleaved by both enzymes, albeit not as effectively as CTB glycopeptides. Neither enzyme requires the Asn-Xaa-(Ser/Thr) sequence (required for N-glycosylation) for activity. Glycoamidase A could even hydrolyze a Gln-bound CTB glycopeptide, whereas the action of glycoamidase F on this substrate is minimal. While glycoamidase A could act on CTB dipeptides, glycoamidase F preferred a tripeptide or longer. The Km and Vmax values of glycoamidase A for t-butoxycarbonyl-(CTB)-Asn-Ala-Ser-OMe were 2.1 mM and 0.66 micromol/min/mg, respectively. A natural glycodipeptide, Man9-GlcNAc2-Asn-Phe, was also completely hydrolyzed by glycoamidase A.

  17. NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

    PubMed Central

    Dunn, Michael F.

    2013-01-01

    Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR

  18. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

    PubMed

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens

    2012-03-07

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.

  19. COG Complex Complexities: Detailed Characterization of a Complete Set of HEK293T Cells Lacking Individual COG Subunits

    PubMed Central

    Bailey Blackburn, Jessica; Pokrovskaya, Irina; Fisher, Peter; Ungar, Daniel; Lupashin, Vladimir V.

    2016-01-01

    The Conserved Oligomeric Golgi complex is an evolutionarily conserved multisubunit tethering complex (MTC) that is crucial for intracellular membrane trafficking and Golgi homeostasis. The COG complex interacts with core vesicle docking and fusion machinery at the Golgi; however, its exact mechanism of action is still an enigma. Previous studies of COG complex were limited to the use of CDGII (Congenital disorders of glycosylation type II)-COG patient fibroblasts, siRNA mediated knockdowns, or protein relocalization approaches. In this study we have used the CRISPR approach to generate HEK293T knock-out (KO) cell lines missing individual COG subunits. These cell lines were characterized for glycosylation and trafficking defects, cell proliferation rates, stability of COG subunits, localization of Golgi markers, changes in Golgi structure, and N-glycan profiling. We found that all KO cell lines were uniformly deficient in cis/medial-Golgi glycosylation and each had nearly abolished binding of Cholera toxin. In addition, all cell lines showed defects in Golgi morphology, retrograde trafficking and sorting, sialylation and fucosylation, but severities varied according to the affected subunit. Lobe A and Cog6 subunit KOs displayed a more severely distorted Golgi structure, while Cog2, 3, 4, 5, and 7 knock outs had the most hypo glycosylated form of Lamp2. These results led us to conclude that every subunit is essential for COG complex function in Golgi trafficking, though to varying extents. We believe that this study and further analyses of these cells will help further elucidate the roles of individual COG subunits and bring a greater understanding to the class of MTCs as a whole. PMID:27066481

  20. Detailed characterization of a Comparative Reactivity Method (CRM) instrument for ambient OH reactivity measurements: experiments vs. modeling

    NASA Astrophysics Data System (ADS)

    Michoud, Vincent; Locoge, Nadine; Dusanter, Sébastien

    2015-04-01

    The Hydroxyl radical (OH) is the main daytime oxidant in the troposphere, leading to the oxidation of Volatile Organic Compounds (VOCs) and the formation of harmful pollutants such as ozone (O3) and Secondary Organic Aerosols (SOA). While OH plays a key role in tropospheric chemistry, recent studies have highlighted that there are still uncertainties associated with the OH budget, i.e the identification of sources and sinks and the quantification of production and loss rates of this radical. It has been demonstrated that ambient measurements of the total OH loss rate (also called total OH reactivity) can be used to identify and reduce these uncertainties. In this context, the Comparative Reactivity Method (CRM), developed by Sinha et al. (ACP, 2008), is a promising technique to measure total OH reactivity in ambient air and has already been used during several field campaigns. This technique relies on monitoring competitive reactions of OH with ambient trace gases and a reference compound (pyrrole) in a sampling reactor to derive ambient OH reactivity. However, this technique requires a complex data processing chain that has yet to be carefully investigated in the laboratory. In this study, we present a detailed characterization of a CRM instrument developed at Mines Douai, France. Experiments have been performed to investigate the dependence of the CRM response on humidity, ambient NOx levels, and the pyrrole-to-OH ratio inside the sampling reactor. Box modelling of the chemistry occurring in the reactor has also been performed to assess our theoretical understanding of the CRM measurement. This work shows that the CRM response is sensitive to both humidity and NOx, which can be accounted for during data processing using parameterizations depending on the pyrrole-to-OH ratio. The agreement observed between laboratory studies and model results suggests a good understanding of the chemistry occurring in the sampling reactor and gives confidence in the CRM

  1. Studies of detailed biofilm characterization on fly ash concrete in comparison with normal and superplasticizer concrete in seawater environments.

    PubMed

    Vishwakarmaa, Vinita; George, R P; Ramachandran, D; Anandkumar, B; Mudalib, U Kamachi

    2014-01-01

    In cooling water systems, many concrete structures in the form of tanks, pillars and reservoirs that come in contact with aggressive seawater are being deteriorated by chemical and biological factors. The nuclear industry has decided to partially replace the Portland cement with appropriate pozzolans such as fly ash, which could densify the matrix and make the concrete impermeable. Three types of concrete mixes, viz., normal concrete (NC), concrete with fly ash and superplasticizer (FA) and concrete with only superplasticizer (SP) were fabricated for short- and long-term exposure studies and for screening out the better concrete in seawater environments. Biofilm characterization studies and microscopic studies showed excellent performance of FA concrete compared to the other two. Laboratory exposure studies in pure cultures of Thiobacillus thiooxidans and Fusarium oxysporum were demonstrated for the inhibition of microbial growth on fly ash. Epifluorescence and scanning electron microscopic studies supported the better performance of the FA specimen. Thus, the present study clearly showed that FA concrete is less prone to biofilm formation and biodeterioration.

  2. Characterization of a laboratory-scale container for freezing protein solutions with detailed evaluation of a freezing process simulation.

    PubMed

    Roessl, Ulrich; Jajcevic, Dalibor; Leitgeb, Stefan; Khinast, Johannes G; Nidetzky, Bernd

    2014-02-01

    A 300-mL stainless steel freeze container was constructed to enable QbD (Quality by Design)-compliant investigations and the optimization of freezing and thawing (F/T) processes of protein pharmaceuticals at moderate volumes. A characterization of the freezing performance was conducted with respect to freezing kinetics, temperature profiling, cryoconcentration, and stability of the frozen protein. Computational fluid dynamic (CFD) simulations of temperature and phase transition were established to facilitate process scaling and process analytics as well as customization of future freeze containers. Protein cryoconcentration was determined from ice-core samples using bovine serum albumin. Activity, aggregation, and structural perturbation were studied in frozen rabbit muscle l-lactic dehydrogenase (LDH) solution. CFD simulations provided good qualitative and quantitative agreement with highly resolved experimental measurements of temperature and phase transition, allowing also the estimation of spatial cryoconcentration patterns. LDH exhibited stability against freezing in the laboratory-scale system, suggesting a protective effect of cryoconcentration at certain conditions. The combination of the laboratory-scale freeze container with accurate CFD modeling will allow deeper investigations of F/T processes at advanced scale and thus represents an important step towards a better process understanding.

  3. Structural characterization of dimeric murine aminoacylase III.

    PubMed

    Ryazantsev, Sergey; Abuladze, Natalia; Newman, Debra; Bondar, Galyna; Kurtz, Ira; Pushkin, Alexander

    2007-05-01

    Aminoacylase III (AAIII) plays an important role in deacetylation of acetylated amino acids and N-acetylated S-cysteine conjugates of halogenated alkenes and alkanes. AAIII, recently cloned from mouse kidney and partially characterized, is a mixture of tetramers and dimers. In the present work, AAIII dimers were purified and shown to be enzymatically active. Limited trypsinolysis showed two domains of approximately 9 and 25 kDa. The three-dimensional structure of the dimer was studied by electron microscopy of negative stained samples and by single-particle reconstruction. A 16A resolution model of the AAIII dimer was created. It has an unusual, cage-like, structure. A realistic AAIII tetramer model was built from two dimers.

  4. The role of structure-to-property-relationships in materials characterization

    SciTech Connect

    Morgner, W.

    2000-07-01

    The paper deals with questions concerning the material characterization for steels in the field of engineering and metallurgy. Based on the structure-to-property-relationships, a procedure is proposed to strengthen the systematical development of methods for nondestructive characterization of materials. The state of the nondestructive characterization of metals is reviewed and applications are described in which adequate macroscopic physical properties are measured in order to characterize the materials state and properties nondestructively. The materials characterization of ball bearing steel and cast iron using multiparametrical approaches is discussed in detail.

  5. Diffractaic acid: Crystalline structure and physicochemical characterization

    NASA Astrophysics Data System (ADS)

    de Castro Fonseca, Jéssica; de Oliveira, Yara Santiago; Bezerra, Beatriz P.; Ellena, Javier; Honda, Neli Kika; Silva, Camilla V. N. S.; da Silva Santos, Noemia Pereira; Santos-Magalhães, Nereide Stela; Ayala, Alejandro Pedro

    2016-08-01

    Diffractaic acid (DA) is a secondary metabolite of lichens that belongs to the chemical class of depsides, and some relevant pharmacological properties are associated with this natural product, such as antioxidant, antiulcerogenic and gastroprotective effects. Considering the relevant biological activities and taking into account that the activities are intrinsically related to the structure, the main goal of this study was to elucidate the structure of diffractaic acid by single crystal X-ray diffraction as well to characterize its physicochemical properties by powder X-ray diffraction, thermal analysis and vibrational spectroscopy. It was observed that DA belongs to the monoclinic crystal system, crystallizing in the space group P21/c with the following cell parameters: a = 18.535(7) Å, b = 4.0439(18) Å, c = 23.964(6) Å, β = 91.55(3)°. The crystal packing is characterized by difractaic acid dimers, which are reflected in the vibrational spectrum. These observations were supported by quantum mechanical calculations.

  6. Thermomechanical characterization and modeling for TSV structures

    SciTech Connect

    Jiang, Tengfei; Zhao, Qiu; Im, Jay; Ho, Paul S.; Ryu, Suk-Kyu; Huang, Rui

    2014-06-19

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  7. Structural characterization of thioether-bridged bacteriocins.

    PubMed

    Lohans, Christopher T; Vederas, John C

    2014-01-01

    Bacteriocins are a group of ribosomally synthesized antimicrobial peptides produced by bacteria, some of which are extensively post-translationally modified. Some bacteriocins, namely the lantibiotics and sactibiotics, contain one or more thioether bridges. However, these modifications complicate the structural elucidation of these bacteriocins using conventional techniques. This review will discuss the techniques and strategies that have been applied to determine the primary structures of lantibiotics and sactibiotics. A major challenge is to identify the topology of thioether bridges in these peptides (i.e., which amino-acid residues are involved in which bridges). Edman degradation, NMR spectroscopy and tandem MS have all been commonly applied to characterize these bacteriocins, but can be incompatible with the post-translational modifications present. Chemical modifications to the modified residues, such as desulfurization and reduction, make the treated bacteriocins more compatible to analysis by these standard peptide analytical techniques. Despite their differences in structure, similar strategies have proved useful to study the structures of both lantibiotics and sactibiotics.

  8. Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores

    DTIC Science & Technology

    2011-04-01

    Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores by Keith M. Kirkwood, Eric D. Wetzel, George Bell, Alan M...21005 ARL-RP-0318 April 2011 Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores Keith M. Kirkwood and...Structural Characterization of Cephalopod Chromatophores 5a. CONTRACT NUMBER ORISE Contract 120-1120-99 (GHIORSE) 5b. GRANT NUMBER 5c. PROGRAM

  9. Hierarchical structures of amorphous solids characterized by persistent homology

    PubMed Central

    Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G.; Matsue, Kaname; Nishiura, Yasumasa

    2016-01-01

    This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods. PMID:27298351

  10. Beta environmental fine structure characterization of defects

    NASA Astrophysics Data System (ADS)

    Benedek, G.; Fiorini, E.; Giuliani, A.; Milani, P.; Monfardini, A.; Nucciotti, A.; Prandoni, M. L.; Sancrotti, M.

    1999-04-01

    The fine structure of beta emission (BEFS) due to the interference with the scattered waves from neighboring atoms, analogous to EXAFS, is known to produce oscillations in the Kurie plot. Here we suggest the use of BEFS for characterizing the lattice environment of β-emitting defects located at a distance from the crystal surface not exceeding the mean free path of β-electrons. Examples of defective structures in semiconductors whose atomic arrangement could be conveniently studied with BEFS are tritium-passivated dangling bonds, β-radioactive ions implanted in the crystal lattice or segregated at extended defects such as dislocations, grain boundaries or radiation damage. Also 14C-doped diamond-like materials and other exotic carbon forms, as well as the atomic environment of ions in metal alloys could be good candidate for BEFS. In this work we have calculated the fractional BEFS modulation for 187Re in its ordinary hcp crystal lattice for which experimental data by Cosulich et al. are available. The good correspondence between theory and experiment permits to conclude that BEFS experiments at low temperature are accessible to the present bolometric detection techniques and can provide an expedient method, as compared to EXAFS, for an accurate structural assessment of extended defects in solids.

  11. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler-Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  12. Characterization of Imposed Ordered Structures in MDPX

    NASA Astrophysics Data System (ADS)

    Hall, Taylor; Thomas, Edward; Konopka, Uwe; Merlino, Robert; Rosenberg, Marlene

    2016-10-01

    It is well understood that the microparticles in complex, or dusty, plasmas will form self-consistent crystalline patterns at the proper plasma parameters. In the Magnetized Dusty Plasma Experiment (MDPX) device, studies have been made of imposed, ordered structuring of the dust particles to a two dimensional grid. At high magnetic field (B >1 Tesla), the dust particles are shown to become spatially oriented to the structure of a wire mesh embedded in an electrically floating, upper electrode while the particles are suspended in a plasma that is generated by the powered, lower electrode in the experiment. With even higher magnetic field (B >2 Tesla), the particles become strongly confined to the mesh pattern with the particles constrained to a quasi-discreet motion that closely follows the mesh pattern. This presentation characterizes the structure of the potential energy well in which the dust particles are trapped through observation of particle motion and measurement of the thermal properties of the particles. This work is supported by funding from the U. S. Department of Energy Grant Number DE - SC0010485 and the NASA/Jet Propulsion Laboratory, JPL-1543114.

  13. Understanding the structure of skill through a detailed analysis of Individuals' performance on the Space Fortress game.

    PubMed

    Towne, Tyler J; Boot, Walter R; Ericsson, K Anders

    2016-09-01

    In this paper we describe a novel approach to the study of individual differences in acquired skilled performance in complex laboratory tasks based on an extension of the methodology of the expert-performance approach (Ericsson & Smith, 1991) to shorter periods of training and practice. In contrast to more traditional approaches that study the average performance of groups of participants, we explored detailed behavioral changes for individual participants across their development on the Space Fortress game. We focused on dramatic individual differences in learning and skill acquisition at the individual level by analyzing the archival game data of several interesting players to uncover the specific structure of their acquired skill. Our analysis revealed that even after maximal values for game-generated subscores were reached, the most skilled participant's behaviors such as his flight path, missile firing, and mine handling continued to be refined and improved (Participant 17 from Boot et al., 2010). We contrasted this participant's behavior with the behavior of several other participants and found striking differences in the structure of their performance, which calls into question the appropriateness of averaging their data. For example, some participants engaged in different control strategies such as "world wrapping" or maintaining a finely-tuned circular flight path around the fortress (in contrast to Participant 17's angular flight path). In light of these differences, we raise fundamental questions about how skill acquisition for individual participants should be studied and described. Our data suggest that a detailed analysis of individuals' data is an essential step for generating a general theory of skill acquisition that explains improvement at the group and individual levels.

  14. Structural characterization of copolymer embedded magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Nedelcu, G. G.; Nastro, A.; Filippelli, L.; Cazacu, M.; Iacob, M.; Rossi, C. Oliviero; Popa, A.; Toloman, D.; Dobromir, M.; Iacomi, F.

    2015-10-01

    Small magnetic nanoparticles (Fe3O4) were synthesized by co-precipitation and coated by emulsion polymerization with poly(methyl methacrylate-co-acrylic acid) (PMMA-co-AAc) to create surface functional groups that can attach drug molecules and other biomolecules. The coated and uncoated magnetite nanoparticles were stored for two years in normal closed ships and than characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, vibrating sample magnetometry, and electron paramagnetic resonance spectroscopy. The solid phase transformation of magnetite to maghemite, as well as an increase in particle size were evidenced for the uncoated nanoparticles. The coated nanoparticles preserved their magnetite structure and magnetic properties. The influences of monomers and surfactant layers on interactions between the magnetic nanoparticles evidenced that the thickness of the polymer has a significant effect on magnetic properties.

  15. Electro-mechanical characterization of structural supercapacitors

    NASA Astrophysics Data System (ADS)

    Gallagher, T.; LaMaster, D.; Ciocanel, C.; Browder, C.

    2012-04-01

    The paper presents electrical and mechanical properties of structural supercapacitors and discusses limitations associated with the approach taken for the electrical properties evaluation. The structural supercapacitors characterized in this work had the electrodes made of carbon fiber weave, separator made of several cellulose based products, and the solid electrolyte made as PEGDGE based polymer blend. The reported electrical properties include capacitance and leakage resistance; the former was measured using cyclic voltammetry. Mechanical properties have been evaluated thorough tensile and three point bending tests performed on structural supercapacitor coupons. The results indicate that the separator material plays an important role on the electrical as well as mechanical properties of the structural capacitor, and that Celgard 3501 used as separator leads to most benefits for both mechanical and electrical properties. Specific capacitance and leakage resistance as high as 1.4kF/m3 and 380kΩ, respectively, were achieved. Two types of solid polymer electrolytes were used in fabrication, with one leading to higher and more consistent leakage resistance values at the expense of a slight decrease in specific capacitance when compared to the other SPE formulation. The ultimate tensile strength and modulus of elasticity of the developed power storage composite were evaluated at 466MPa and 18.9MPa, respectively. These values are 58% and 69% of the tensile strength and modulus of elasticity values measured for a single layer composite material made with the same type of carbon fiber and with a West System 105 epoxy instead of solid polymer electrolyte.

  16. Characterizing the structure of topological insulator thin films

    SciTech Connect

    Richardella, Anthony; Kandala, Abhinav; Lee, Joon Sue; Samarth, Nitin

    2015-08-01

    We describe the characterization of structural defects that occur during molecular beam epitaxy of topological insulator thin films on commonly used substrates. Twinned domains are ubiquitous but can be reduced by growth on smooth InP (111)A substrates, depending on details of the oxide desorption. Even with a low density of twins, the lattice mismatch between (Bi, Sb){sub 2}Te{sub 3} and InP can cause tilts in the film with respect to the substrate. We also briefly discuss transport in simultaneously top and back electrically gated devices using SrTiO{sub 3} and the use of capping layers to protect topological insulator films from oxidation and exposure.

  17. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide

    PubMed Central

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M.; Corsaro, Maria Michela

    2017-01-01

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry. PMID:28273861

  18. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide.

    PubMed

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M; Corsaro, Maria Michela

    2017-03-04

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry.

  19. Dynamism & Detail

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2004-01-01

    New material discovered in the study of cell research is presented for the benefit of biology teachers. Huge amounts of data are being generated in fields like cellular dynamics, and it is felt that people's understanding of the cell is becoming much more complex and detailed.

  20. Fabrication and Characterization of Graded Cu-Doped Be Shells - Details and Documentation of Our First Attempt

    SciTech Connect

    Gunther, J; McElfresh, M; Alford, C; Huang, H; Cook, R

    2004-10-08

    We have fabricated by sputtering and characterized a set of step-graded Cu-doped Be capsules. The capsules were made with Cu doped layers of about 0.35 and 0.70 atom % Cu. The total thickness of the coating is about 100 {micro}m. Capsules were removed from the coater for characterization after each layer was deposited. Our ability to produce doped layers is confirmed, and our ability to control the level of doping is excellent. A variety of characterization techniques, both destructive and non-destructive were explored. The surface finish of the sample capsules removed after each layer progressively got rougher, it is likely that polishing will be necessary to produce capsules that will meet surface specifications. We have learned a great deal from this first effort, both in terms of coating technology and capsule characterization. We are now implementing several changes in the coating system based in part upon our experience with this first effort. The next graded capsule run should begin near the end of October.

  1. Structural characterization of submerged granular packings.

    PubMed

    Jakšić, Z M; Šćepanović, J R; Lončarević, I; Budinski-Petković, Lj; Vrhovac, S B; Belić, A

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  2. Structural characterization of submerged granular packings

    NASA Astrophysics Data System (ADS)

    Jakšić, Z. M.; Šćepanović, J. R.; Lončarević, I.; Budinski-Petković, Lj.; Vrhovac, S. B.; Belić, A.

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  3. Detailed Structural and Quantitative Analysis Reveals the Spatial Organization of the Cell Walls of in Vivo Grown Mycobacterium leprae and in Vitro Grown Mycobacterium tuberculosis*

    PubMed Central

    Bhamidi, Suresh; Scherman, Michael S.; Jones, Victoria; Crick, Dean C.; Belisle, John T.; Brennan, Patrick J.; McNeil, Michael R.

    2011-01-01

    The cell wall of mycobacteria consists of an outer membrane, analogous to that of Gram-negative bacteria, attached to the peptidoglycan (PG) via a connecting polysaccharide arabinogalactan (AG). Although the primary structure of these components is fairly well deciphered, issues such as the coverage of the PG layer by covalently attached mycolates in the outer membrane and the spatial details of the mycolic acid attachment to the arabinan have remained unknown. It is also not understood how these components work together to lead to the classical acid-fast staining of mycobacteria. Because the majority of Mycobacterium tuberculosis bacteria in established experimental animal infections are acid-fast negative, clearly cell wall changes are occurring. To address both the spatial properties of mycobacterial cell walls and to begin to study the differences between bacteria grown in animals and cultures, the cell walls of Mycobacterium leprae grown in armadillos was characterized and compared with that of M. tuberculosis grown in culture. Most fundamentally, it was determined that the cell wall of M. leprae contained significantly more mycolic acids attached to PG than that of in vitro grown M. tuberculosis (mycolate:PG ratios of 21:10 versus 16:10, respectively). In keeping with this difference, more arabinogalactan (AG) molecules, linking the mycolic acids to PG, were found. Differences in the structures of the AG were also found; the AG of M. leprae is smaller than that of M. tuberculosis, although the same basic structural motifs are retained. PMID:21555513

  4. Detailed structural and quantitative analysis reveals the spatial organization of the cell walls of in vivo grown Mycobacterium leprae and in vitro grown Mycobacterium tuberculosis.

    PubMed

    Bhamidi, Suresh; Scherman, Michael S; Jones, Victoria; Crick, Dean C; Belisle, John T; Brennan, Patrick J; McNeil, Michael R

    2011-07-01

    The cell wall of mycobacteria consists of an outer membrane, analogous to that of gram-negative bacteria, attached to the peptidoglycan (PG) via a connecting polysaccharide arabinogalactan (AG). Although the primary structure of these components is fairly well deciphered, issues such as the coverage of the PG layer by covalently attached mycolates in the outer membrane and the spatial details of the mycolic acid attachment to the arabinan have remained unknown. It is also not understood how these components work together to lead to the classical acid-fast staining of mycobacteria. Because the majority of Mycobacterium tuberculosis bacteria in established experimental animal infections are acid-fast negative, clearly cell wall changes are occurring. To address both the spatial properties of mycobacterial cell walls and to begin to study the differences between bacteria grown in animals and cultures, the cell walls of Mycobacterium leprae grown in armadillos was characterized and compared with that of M. tuberculosis grown in culture. Most fundamentally, it was determined that the cell wall of M. leprae contained significantly more mycolic acids attached to PG than that of in vitro grown M. tuberculosis (mycolate:PG ratios of 21:10 versus 16:10, respectively). In keeping with this difference, more arabinogalactan (AG) molecules, linking the mycolic acids to PG, were found. Differences in the structures of the AG were also found; the AG of M. leprae is smaller than that of M. tuberculosis, although the same basic structural motifs are retained.

  5. Antifreeze (glyco)protein mimetic behavior of poly(vinyl alcohol): detailed structure ice recrystallization inhibition activity study.

    PubMed

    Congdon, Thomas; Notman, Rebecca; Gibson, Matthew I

    2013-05-13

    This manuscript reports a detailed study on the ability of poly(vinyl alcohol) to act as a biomimetic surrogate for antifreeze(glyco)proteins, with a focus on the specific property of ice-recrystallization inhibition (IRI). Despite over 40 years of study, the underlying mechanisms that govern the action of biological antifreezes are still poorly understood, which is in part due to their limited availability and challenging synthesis. Poly(vinyl alcohol) (PVA) has been shown to display remarkable ice recrystallization inhibition activity despite its major structural differences to native antifreeze proteins. Here, controlled radical polymerization is used to synthesize well-defined PVA, which has enabled us to obtain the first quantitative structure-activity relationships, to probe the role of molecular weight and comonomers on IRI activity. Crucially, it was found that IRI activity is "switched on" when the polymer chain length increases from 10 and 20 repeat units. Substitution of the polymer side chains with hydrophilic or hydrophobic units was found to diminish activity. Hydrophobic modifications to the backbone were slightly more tolerated than side chain modifications, which implies an unbroken sequence of hydroxyl units is necessary for activity. These results highlight that, although hydrophobic domains are key components of IRI activity, the random inclusion of addition hydrophobic units does not guarantee an increase in activity and that the actual polymer conformation is important.

  6. Structural Characterization of Bimetallic Nanocrystal Electrocatalysts

    SciTech Connect

    Cullen, David A

    2016-01-01

    Late transition metal nanocrystals find applications in heterogeneous catalysis such as plasmon-enhanced catalysis and as electrode materials for fuel cells, a zero-emission and sustainable energy technology. Their commercial viability for automotive transportation has steadily increased in recent years, almost exclusively due to the discovery of more efficient bimetallic nanocatalysts for the oxygen reduction reaction (ORR) at the cathode. Despite improvements to catalyst design, achieving high activity while maintaining durability is essential to further enhance their performance for this and other important applications in catalysis. Electronic effects arising from the generation of metal-metal interfaces, from plasmonic metals, and from lattice distortions, can vastly improve sorption properties at catalytic surfaces, while increasing durability.[1] Multimetallic lattice-strained nanoparticles are thus an interesting opportunity for fundamental research.[2,3] A colloidal synthesis approach is demonstrated to produce AuPd alloy and Pd@Au core-shell nanoicosahedra as catalysts for electro-oxidations. The nanoparticles are characterized using aberration-corrected scanning transmission electron microscopy (ac-STEM) and large solid angle energy dispersive X-ray spectroscopy (EDS) on an FEI Talos 4-detector STEM/EDS system. Figure 1 shows bright-field (BF) and high-angle annular dark-field (HAADF) ac-STEM images of the alloy and core-shell nanoicosahedra together with EDS line-scans and elemental maps. These structures are unique in that the presence of twin boundaries, alloying, and core-shell morphology could create highly strained surfaces and interfaces. The shell thickness of the core-shell structures observed in HAADF-STEM images is tuned by adjusting the ratio between metal precursors (Figure 2a-f) to produce shells ranging from a few to several monolayers. Specific activity was measured in ethanol electro-oxidation to examine the effect of shell thickness on

  7. Detection and Characterization of R Loop Structures.

    PubMed

    Boque-Sastre, Raquel; Soler, Marta; Guil, Sonia

    2017-01-01

    R loops are special three stranded nucleic acid structures that comprise a nascent RNA hybridized with the DNA template strand, leaving a non-template DNA single-stranded. More specifically, R loops form in vivo as G-rich RNA transcripts invade the DNA duplex and anneal to the template strand to generate an RNA:DNA hybrid, leaving the non-template, G-rich DNA strand in a largely single-stranded conformation (Aguilera and Garcia-Muse, Mol Cell 46:115-124, 2012).DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. RNA-DNA hybrids influence genomic instability, and growing evidence points to an important role for R loops in active gene expression regulation (Ginno et al., Mol Cell 45, 814-825, 2012; Sun et al., Science 340: 619-621, 2013; Bhatia et al., Nature 511, 362-365, 2014). Analysis of the occurrence of such structures is therefore of increasing relevance and herein we describe methods for the in vivo and in vitro identification and characterization of R loops in mammalian systems.R loops (DNA:RNA hybrids and the associated single-stranded DNA) have been traditionally associated with threats to genome integrity, making some regions of the genome more prone to DNA-damaging and mutagenic agents. Initially considered to be rare byproducts of transcription, over the last decade accumulating evidence has pointed to a new view in which R loops form more frequently than previously thought. The R loop field has become an increasingly expanded area of research, placing these structures as a major threat to genome stability but also as potential regulators of gene expression. Special interest has arisen as they have also been linked to a variety of diseases, including neurological disorders and cancer, positioning them as potential therapeutic targets [5].

  8. Structural Characterization of Crystalline Ice Nanoclusters

    NASA Technical Reports Server (NTRS)

    Blake, David

    2000-01-01

    Water ice nanoclusters are useful analogs for studying a variety of processes that occur within icy grains in the extraterrestrial environment. The surface of ice nanoclusters prepared in the laboratory is similar to the surface of interstellar ice grains. In cold molecular clouds, the silicate cores of interstellar grains are typically approx. 100 nm in diameter and have a coating of impure amorphous water ice. Depositional, thermal and radiolytic processes leave the surface and subsurface molecules in a disordered state. In this state, structural defects become mobile and reactions of trapped gases and small molecules can occur. The large surface area of nanocluster deposits relative to their bulk allows for routine observation of such surface-mediated processes. Furthermore, the disordered surface and subsurface layers in nanocluster deposits mimic the structure of amorphous ice rinds found on interstellar dust grains. Transmission Electron Microscopy (TEM has been used tn characterize the crystallinity, growth mechanism, and size distribution of nanoclusters formed from a mixture of water vapor with an inert carrier gas that has been rapidly cooled to 77K. E M imaging reveals a Gaussian size distribution around a modal diameter that increases from approx. 15 to 30 nm as the percentage of water vapor within the mixture increases from 0.5 to 2.007, respectively . TEM bright and dark field imaging also reveals the crystalline nature of the clusters. h4any of the clusters show a mosaic structure in which crystalline domains originate at the center Other images show mirror planes that are separated by approx. 10 nm. Electron diffraction patterns of these clusters show that the clusters are composed of cubic ice with only a small hexagonal component. Further, the crystalline domain size is approximately the same as the modal diameter suggesting that the clusters are single crystals.

  9. Characterization of adhesive from oysters: A structural and compositional study

    NASA Astrophysics Data System (ADS)

    Alberts, Erik

    The inability for man-made adhesives to set in wet or humid environments is an ongoing challenging the design of biomedical and marine adhesive materials. However, we see that nature has already overcome this challenge. Mussels, barnacles, oysters and sandcastle worms all have unique mechanisms by which they attach themselves to surfaces. By understanding what evolution has already spent millions of years perfecting, we can design novel adhesive materials inspired by nature's elegant designs. The well-studied mussel is currently the standard for design of marine inspired biomimetic polymers. In the work presented here, we aim to provide new insights into the adhesive produced by the eastern oyster, Crassostrea virginica. Unlike the mussel, which produces thread-like plaques comprised of DOPA containing-protein, the oyster secretes an organic-inorganic hybrid adhesive as it settles and grows onto a surface. This form of adhesion renders the oyster to be permanently fixed in place. Over time, hundreds of thousands of oyster grow and agglomerate to form extensive reef structures. These reefs are not only essential to survival of the oyster, but are also vital to intertidal ecosystems. While the shell of the oyster has been extensively studied, curiously, only a few conflicting insights have been made into the nature of the adhesive and contact zone between shell and substrate, and even lesfs information has been ascertained on organic and inorganic composition. In this work, we provide microscopy and histochemical studies to characterize the structure and composition of the adhesive, using oyster in the adult and juvenile stages of life. Preliminary work on extracting and characterizing organic components through collaborative help with solid-state NMR (SSNMR) and proteomics are also detailed here. We aim to provide a full, comprehensive characterization of oyster adhesive so that in the future, we may apply what we learn to the design of new materials.

  10. Academic detailing.

    PubMed

    Shankar, P R; Jha, N; Piryani, R M; Bajracharya, O; Shrestha, R; Thapa, H S

    2010-01-01

    There are a number of sources available to prescribers to stay up to date about medicines. Prescribers in rural areas in developing countries however, may not able to access some of them. Interventions to improve prescribing can be educational, managerial, and regulatory or use a mix of strategies. Detailing by the pharmaceutical industry is widespread. Academic detailing (AD) has been classically seen as a form of continuing medical education in which a trained health professional such as a physician or pharmacist visits physicians in their offices to provide evidence-based information. Face-to-face sessions, preferably on an individual basis, clear educational and behavioural objectives, establishing credibility with respect to objectivity, stimulating physician interaction, use of concise graphic educational materials, highlighting key messages, and when possible, providing positive reinforcement of improved practices in follow-up visits can increase success of AD initiatives. AD is common in developed countries and certain examples have been cited in this review. In developing countries the authors have come across reports of AD in Pakistan, Sudan, Argentina and Uruguay, Bihar state in India, Zambia, Cuba, Indonesia and Mexico. AD had a consistent, small but potentially significant impact on prescribing practices. AD has much less resources at its command compared to the efforts by the industry. Steps have to be taken to formally start AD in Nepal and there may be specific hindering factors similar to those in other developing nations.

  11. A survey of molecular details in the human pineal gland in the light of phylogeny, structure, function and chronobiological diseases.

    PubMed

    Stehle, Jörg H; Saade, Anastasia; Rawashdeh, Oliver; Ackermann, Katrin; Jilg, Antje; Sebestény, Tamás; Maronde, Erik

    2011-08-01

    The human pineal gland is a neuroendocrine transducer that forms an integral part of the brain. Through the nocturnally elevated synthesis and release of the neurohormone melatonin, the pineal gland encodes and disseminates information on circadian time, thus coupling the outside world to the biochemical and physiological internal demands of the body. Approaches to better understand molecular details behind the rhythmic signalling in the human pineal gland are limited but implicitly warranted, as human chronobiological dysfunctions are often associated with alterations in melatonin synthesis. Current knowledge on melatonin synthesis in the human pineal gland is based on minimally invasive analyses, and by the comparison of signalling events between different vertebrate species, with emphasis put on data acquired in sheep and other primates. Together with investigations using autoptic pineal tissue, a remnant silhouette of premortem dynamics within the hormone's biosynthesis pathway can be constructed. The detected biochemical scenario behind the generation of dynamics in melatonin synthesis positions the human pineal gland surprisingly isolated. In this neuroendocrine brain structure, protein-protein interactions and nucleo-cytoplasmic protein shuttling indicate furthermore a novel twist in the molecular dynamics in the cells of this neuroendocrine brain structure. These findings have to be seen in the light that an impaired melatonin synthesis is observed in elderly and/or demented patients, in individuals affected by Alzheimer's disease, Smith-Magenis syndrome, autism spectrum disorder and sleep phase disorders. Already, recent advances in understanding signalling dynamics in the human pineal gland have significantly helped to counteract chronobiological dysfunctions through a proper restoration of the nocturnal melatonin surge.

  12. LASER BIOLOGY AND MEDICINE: Visualisation of details of a complicated inner structure of model objects by the method of diffusion optical tomography

    NASA Astrophysics Data System (ADS)

    Tret'yakov, Evgeniy V.; Shuvalov, Vladimir V.; Shutov, I. V.

    2002-11-01

    An approximate algorithm is tested for solving the problem of diffusion optical tomography in experiments on the visualisation of details of the inner structure of strongly scattering model objects containing scattering and semitransparent inclusions, as well as absorbing inclusions located inside other optical inhomogeneities. The stability of the algorithm to errors is demonstrated, which allows its use for a rapid (2 — 3 min) image reconstruction of the details of objects with a complicated inner structure.

  13. Th-substituted SmFeAsO: Structural details and superconductivity with Tc above 50 K

    NASA Astrophysics Data System (ADS)

    Zhigadlo, N. D.; Katrych, S.; Weyeneth, S.; Puzniak, R.; Moll, P. J. W.; Bukowski, Z.; Karpinski, J.; Keller, H.; Batlogg, B.

    2010-08-01

    We report structural, magnetic, and transport properties of polycrystalline samples and single crystals of superconducting Sm1-xThxFeAsO with maximal Tc above 50 K, prepared under high pressure. Bulk superconducting samples do not undergo a structural phase transition from tetragonal to orthorhombic symmetry at low temperatures. The unit-cell parameters a and c shrink with Th substitution and the fractional atomic coordinate of the As site zAs remains almost unchanged while that of Sm/Th zSm/Th increases. Upon warming from 5 to 295 K the increase in the FeAs layer thickness is dominant, while the changes in the other structural building blocks are minor, and they compensate each other, since the As-Sm/Th distance contracts by about the same amount as the O-Sm/Th expands. The polycrystalline and single-crystalline samples are characterized by a full diamagnetic response in low magnetic field, by a high intergrain critical current density for polycrystalline samples, and by a critical current density on the order of 8×105A/cm2 for single crystals at 2 K in fields up to 7 T. The magnetic penetration depth anisotropy γλ increases with decreasing temperature, in a similar way to that of SmFeAsO1-xFy single crystals. The upper critical field estimated from resistance measurements is anisotropic with slopes of ˜5.4T/K ( H∥ab plane) and ˜2.7T/K ( H∥c axis), at temperatures sufficiently far below Tc . The low-temperature upper critical field anisotropy γH is in the range of ˜2 , consistent with the tendency of a decreasing γH with decreasing temperature, previously reported for SmFeAsO1-xFy single crystals.

  14. Detailed immunohistochemical characterization of temporal and spatial progression of Alzheimer's disease-related pathologies in male triple-transgenic mice

    PubMed Central

    Mastrangelo, Michael A; Bowers, William J

    2008-01-01

    Background Several transgenic animal models genetically predisposed to develop Alzheimer's disease (AD)-like pathology have been engineered to facilitate the study of disease pathophysiology and the vetting of potential disease-modifying therapeutics. The triple transgenic mouse model of AD (3xTg-AD) harbors three AD-related genetic loci: human PS1M146V, human APPswe, and human tauP301L. These mice develop both amyloid plaques and neurofibrillary tangle-like pathology in a progressive and age-dependent manner, while these pathological hallmarks are predominantly restricted to the hippocampus, amygdala, and the cerebral cortex the main foci of AD neuropathology in humans. This model represents, at present, one of the most advanced preclinical tools available and is being employed ever increasingly in the study of mechanisms underlying AD, yet a detailed regional and temporal assessment of the subtleties of disease-related pathologies has not been reported. Methods and results In this study, we immunohistochemically documented the evolution of AD-related transgene expression, amyloid deposition, tau phosphorylation, astrogliosis, and microglial activation throughout the hippocampus, entorhinal cortex, primary motor cortex, and amygdala over a 26-month period in male 3xTg-AD mice. Intracellular amyloid-beta accumulation is detectable the earliest of AD-related pathologies, followed temporally by phospho-tau, extracellular amyloid-beta, and finally paired helical filament pathology. Pathology appears to be most severe in medial and caudal hippocampus. While astrocytic staining remains relatively constant at all ages and regions assessed, microglial activation appears to progressively increase temporally, especially within the hippocampal formation. Conclusion These data fulfill an unmet need in the ever-widening community of investigators studying 3xTg-AD mice and provide a foundation upon which to design future experiments that seek to examine stage-specific disease

  15. Crump Geyser Exploration and Drilling Project. High Precision Geophysics and Detailed Structural Exploration and Slim Well Drilling

    SciTech Connect

    Fairbank, Brian D.; Smith, Nicole

    2015-06-10

    The Crump Geyser Exploration and Drilling Project – High Precision Geophysics and Detailed Structural Exploration and Slim Well Drilling ran from January 29, 2010 to September 30, 2013. During Phase 1 of the project, collection of all geophysical surveys was completed as outlined in the Statement of Project Objectives. In addition, a 5000-foot full sized exploration well was drilled by Ormat, and preexisting drilling data was discovered for multiple temperature gradient wells within the project area. Three dimensional modeling and interpretation of results from the geophysical surveys and drilling data gave confidence to move to the project into Phase 2 drilling. Geological and geophysical survey interpretations combined with existing downhole temperature data provided an ideal target for the first slim-hole drilled as the first task in Phase 2. Slim-hole 35-34 was drilled in September 2011 and tested temperature, lithology, and permeability along the primary range-bounding fault zone near its intersection with buried northwest-trending faults that have been identified using geophysical methods. Following analysis of the results of the first slim-hole 35-34, the second slim hole was not drilled and subsequent project tasks, including flowing differential self-potential (FDSP) surveys that were designed to detail the affect of production and injection on water flow in the shallow aquifer, were not completed. NGP sold the Crump project to Ormat in August 2014, afterwards, there was insufficient time and interest from Ormat available to complete the project objectives. NGP was unable to continue managing the award for a project they did not own due to liability issues and Novation of the award was not a viable option due to federal award timelines. NGP submitted a request to mutually terminate the award on February 18, 2015. The results of all of the technical surveys and drilling are included in this report. Fault interpretations from surface geology, aeromag

  16. On the structure and dynamics of Ellerman bombs. Detailed study of three events and modelling of Hα

    NASA Astrophysics Data System (ADS)

    Bello González, N.; Danilovic, S.; Kneer, F.

    2013-09-01

    Aims: We study the structure and dynamics of three Ellerman bombs (EBs) observed in an evolving active region. Methods: The active region NOAA 11271 was observed with the Vacuum Tower Telescope at Observatorio del Teide/Tenerife on August 18, 2011. We used the two-dimensional Triple Etalon SOlar Spectrometer (TESOS) to obtain time sequences of the active region and of EBs in Hα at a cadence of 15 s. Simultaneously, we obtained full Stokes profiles with the Tenerife Infrared Polarimeter (TIP II) in the two magnetically sensitive Fe i infrared lines (IR) at 1.56 μ, scanning spatial sections of the area with cadences of 28-46 s. The Hα data were reconstructed with speckle methods to study the evolution of the atmospheric stratification. Two methods were used to extract magnetic field information from the IR Stokes profiles: 1) fitting of the (Q,U,V) profiles by Gaussians; and 2) applying the Milne-Eddington approximation, assuming two separate magnetic structures in the resolution element and fitting by trial and error some profiles from the EB areas. Data from SDO-HMI and -AIA were also used. We performed two-dimensional (2D) non-LTE radiative transfer calculations of Hα in parameterised models of EBs. Results: The three EBs studied in detail occurred in a complex active region near sunspots. They were very bright with a factor of 1.5-2.8 brighter than the nearby area. They lived for 1/2 h and longer. They were related to broadband faculae, but the latter were not the brightest features in the field of view. The EBs occurred in magnetic field configurations with opposite polarity close together. One EB was located at the outskirts of a penumbra of a complex sunspot and showed repeated "flaring" in SDO-AIA data. Another was close to a strong field patch and moved into this during the end of its lifetime. The third EB showed clear changes of field structure during the time it was observed. We obtained from the 2D modelling that heating and increase in Hα opacity

  17. A Detailed Protocol for Characterizing the Murine C1498 Cell Line and its Associated Leukemia Mouse Model

    PubMed Central

    Mopin, Alexia; Driss, Virginie; Brinster, Carine

    2016-01-01

    The intravenous injection of C1498 cells into syngeneic or congenic mice has been performed since 1941. These injections result in the development of acute leukemia. However, the nature of this disease has not been well documented in the literature. Here, we provide a technical protocol for characterizing C1498 cells in vitro and for determining the nature of the induced leukemia in vivo. The first part of this procedure is focused on determining the hematopoietic lineage and the stage of differentiation of cultured C1498 cells. To achieve this, multi-parametric flow cytometric staining is used to detect hematopoietic cell markers. Immunofluorescence microscopy, cytochemistry and a May-Grünwald Giemsa staining are then performed to assess the expression of myeloperoxidase, the activity of esterases and cellular morphology, respectively. The second part of this protocol is dedicated to describing the leukemia disease that is induced in vivo. The latter can be achieved by determining the frequencies of leukemic and inherent cells in the blood, hematopoietic organs (e.g., bone marrow and spleen) and non-lymphoid tissues (e.g., the liver and lungs) using specific staining and flow cytometry analyses. The nature of the leukemia is then confirmed using May-Grünwald Giemsa staining and staining for specific esterases in the bone marrow. Here, we present the results that were obtained using this protocol in age-matched C1498- and PBS-injected mice. PMID:27768040

  18. Statistical characterization of phenolic-novolak structures

    NASA Technical Reports Server (NTRS)

    Parker, J. A.; Winkler, E. L.

    1971-01-01

    Three statistical methods of general validity are valuable for characterizing any polymer which results from chain polymerization of multifunctional branching monomers linked through bifunctional monomers.

  19. Detailed crustal structure in the area of the southern Apennines-Calabrian Arc border from local earthquake tomography

    NASA Astrophysics Data System (ADS)

    Totaro, C.; Koulakov, I.; Orecchio, B.; Presti, D.

    2014-12-01

    We present a new seismic velocity model for the southern Apennines-Calabrian Arc border region with the aim to better define the crustal structures at the northern edge of the Ionian subduction zone. This sector also includes the Pollino Mts. area, where a seismic sequence of thousands of small to moderate earthquakes has been recorded between spring 2010 and 2013. In this sector a seismic gap was previously hypothesized by paleoseismological evidences associated with the lack of major earthquakes in historical catalogs. To perform the tomographic inversion we selected ca. 3600 earthquakes that have occurred in the last thirty years and recorded by permanent and temporary networks managed by INGV and Calabria University. Using for the first time the Local Tomography Software for passive tomography inversion (LOTOS hereinafter) to crustal analysis in southern Italy, we have computed the distribution of Vp, Vs, and the Vp/Vs ratio. The obtained velocity model, jointly evaluated with results of synthetic modeling, as well as with the hypocenter distribution and geological information, gives us new constraints on the geodynamical and structural knowledge of the study area. The comparison between the shallow tomography sections and surface geology shows good correlation between velocity patterns and the main geological features of the study area. In the upper crust a low-velocity anomaly of P- and S-waves is detectable beneath the Pollino Mts. area and seems to separate the Calabrian and southern Apennines domains, characterized by higher velocities. The distributions of high Vp/Vs ratio, representing strongly fractured rocks with likely high fluid content, clearly correlate with areas of significant seismicity. In the lower crust we detect a clear transition from high to low seismic velocities in correspondence with the Tyrrhenian coast of the study area, which may represent the transition from the thinner Tyrrhenian crust to the thicker one beneath Calabria. In this

  20. Structural characterization of soy protein nanoparticles from high shear microfluidization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soy protein nanoparticles were produced with a microfluidizer and characterized in terms of particle size, size distribution, morphology, rheological properties, and aggregate structure. Three stages of structure breakdown were observed when the soy protein dispersion was passed through the microflu...

  1. Detailed characterization of the kinetic performance of first and second generation silica monolithic columns for reversed-phase chromatography separations.

    PubMed

    Cabooter, Deirdre; Broeckhoven, Ken; Sterken, Roman; Vanmessen, Alison; Vandendael, Isabelle; Nakanishi, Kazuki; Deridder, Sander; Desmet, Gert

    2014-01-17

    The kinetic performance of commercially available first generation and prototype second generation silica monoliths has been investigated for 2.0mm and 3.0-3.2mm inner diameter columns. It is demonstrated that the altered sol-gel process employed for the production of second generation monoliths results in structures with a smaller characteristic size leading to an improved peak shape and higher efficiencies. The permeability of the columns however, decreases significantly due to the smaller throughpore and skeleton sizes. Scanning electron microscopy pictures suggest the first generation monoliths have cylindrical skeleton branches, whereas the second generation monoliths rather have skeleton branches that resemble a single chain of spherical globules. Using recently established correlations for the flow resistance of cylindrical and globule chain type monolithic structures, it is demonstrated that the higher flow resistance of the second generation monoliths can be entirely attributed to their smaller skeleton sizes, which is also evident from the external porosity that is largely the same for both monolith generations (ɛe∼0.65). The recorded van Deemter plots show a clear improvement in efficiency for the second generation monoliths (minimal plate heights of 13.6-14.1μm for the first and 6.5-8.2μm for the second generation, when assessing the plate count using the Foley-Dorsey method). The corresponding kinetic plots, however, indicate that the much reduced permeability of the second generation monoliths results in kinetic performances (time needed to achieve a given efficiency) which are only better than those of the first generation for plate counts up to N∼45,000. For more complex samples (N≥50,000), the first generation monoliths can intrinsically still provide faster analysis due to their high permeability. It is also demonstrated that - despite the improved efficiency of the second generation monoliths in the practical range of separations (N=10

  2. Structure and mutational analysis of the PhoN protein of Salmonella typhimurium provide insight into mechanistic details.

    PubMed

    Makde, Ravindra D; Mahajan, Suresh K; Kumar, Vinay

    2007-02-27

    The Salmonella typhimurium PhoN protein is a nonspecific acid phosphatase and belongs to the phosphatidic acid phosphatase type 2 (PAP2) superfamily. We report here the crystal structures of phosphate-bound PhoN, the PhoN-tungstate complex, and the T159D mutant of PhoN along with functional characterization of three mutants: L39T, T159D, and D201N. Invariant active site residues, Lys-123, Arg-130, Ser-156, Gly-157, His-158, and Arg-191, interact with phosphate and tungstate oxyanions. Ser-156 also accepts a hydrogen bond from Thr-159. The T159D mutation, surprisingly, severely diminishes phosphatase activity, apparently by disturbing the active site scaffold: Arg-191 is swung out of the active site resulting in conformational changes in His-158 and His-197 residues. Our results reveal a hitherto unknown functional role of Arg-191, namely, restricting the active conformation of catalytic His-158 and His-197 residues. Consistent with the conserved nature of Asp-201 in the PAP2 superfamily, the D201N mutation completely abolished phosphatase activity. On the basis of this observation and in silico analysis we suggest that the crucial mechanistic role of Asp-201 is to stabilize the positive charge on the phosphohistidine intermediate generated by the transfer of phosphoryl to the nucleophile, His-197, located within hydrogen bond distance to the invariant Asp-201. This is in contrast to earlier suggestions that Asp-201 stabilizes His-197 and the His197-Asp201 dyad facilitates formation of the phosphoenzyme intermediate through a charge-relay system. Finally, the L39T mutation in the conserved polyproline motif (39LPPPP43) of dimeric PhoN leads to a marginal reduction in activity, in contrast to the nearly 50-fold reduction observed for monomeric Prevotella intermedia acid phosphatase, suggesting that the varying quaternary structure of PhoN orthologues may have functional significance.

  3. Production and detailed characterization of biologically active olive pollen allergen Ole e 1 secreted by the yeast Pichia pastoris.

    PubMed

    Huecas, S; Villalba, M; González, E; Martínez-Ruiz, A; Rodríguez, R

    1999-04-01

    The glycoprotein Ole e 1 is a significant aeroallergen from the olive tree (Olea europaea) pollen, with great clinical relevance in the Mediterranean area. To produce a biologically active form of recombinant Ole e 1, heterologous expression in the methylotrophic yeast Pichia pastoris was carried out. A cDNA encoding Ole e 1, fused to a Saccharomyces cerevisiae alpha-mating factor prepropeptide using the pPIC9 vector, was inserted into the yeast genome under the control of the AOX1 promoter. After induction with methanol, the protein secreted into the extracellular medium was purified by ion-exchange and size-exclusion chromatography. The structure of the isolated recombinant Ole e 1 was determined by chemical and spectroscopic techniques, and its immunological properties analysed by blotting and ELISA inhibition with Ole e 1-specific monoclonal antibodies and IgE from sera of allergic patients. The allergen was produced at a yield of 60 mg per litre of culture as a homogeneous glycosylated protein of around 18.5 kDa. Recombinant Ole e 1 appears to be properly folded, as it displays spectroscopic properties (CD and fluorescence) and immunological reactivities (IgG binding to monoclonal antibodies sensitive to denaturation and IgE from sera of allergic patients) indistinguishable from those of the natural protein. This approach gives high-yield production of homogeneous and biologically active allergen, which should be useful for scientific and clinical purposes.

  4. Structural characterization of human Uch37

    SciTech Connect

    Burgie, E. Sethe; Bingman, Craig A.; Soni, Ameet B.; Phillips, Jr., George N.

    2012-06-28

    Uch37 is a deubiquitylating enzyme (DUB) that is functionally linked with multiple protein complexes and signal transduction pathways. Uch37 associates with the 26S proteasome through Rpn13 where it serves to remove distal ubiquitin moeities from polyubiquitylated proteins. Uch37's proteasome associated activity was shown to liberate proteins from destruction. However, Uch37 may also specifically facilitate the destruction of inducible nitric oxide synthase and I{kappa}B-{alpha} at the proteasome. Wicks et al. established Uch37's potential to modulate the transforming growth factor-{beta}(TGF-{beta}) signaling cascade, through tis interaction with SMAD7. Yao et al. demonstrated that Uch37 also associates with the Ino80 chromatin-remodeling complex (Ino80 complex), which is involved in DNA repair and transcriptional regulation. Uch37's importance in metazoan development was underscored recently as Uch37 knockouts in mice result in prenatal lethality, where mutant embryos had severe defects in brain development. Protein ubiquitylation is an ATP-dependent post-translational modification that serves to signal a wide variety of cellular processes in eukaryotes. A protein cascade, generally comprising three enzymes, functions to activate, transport and specifically transfer ubiquitin to the targeted protein, culminating in an isopeptide linkage between the {epsilon}-amino group of a target protein's lysysl residue and the ubiquitin's terminal carboxylate. Monoubiquitination plays an important role in histone regulation, endocytosis, and viral budding. Further processing of the target protein may be accomplished by ubiquitylation of the protein on a different lysine, or through the formation of polyubiquitin chains, where the best-characterized outcome is destruction of the polyubiquitin-labeled protein in the proteasome. DUBs catalyze the removal of ubiquitin from proteins. This activity serves to reverse the effects of ubiquitination, permit ubiquitin recycling, or

  5. Structure-based characterization of multiprotein complexes.

    PubMed

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

    2014-07-08

    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.

  6. Carbon nano structures: Production and characterization

    NASA Astrophysics Data System (ADS)

    Beig Agha, Rosa

    L'objectif de ce memoire est de preparer et de caracteriser des nanostructures de carbone (CNS -- Carbon Nanostructures, en licence a l'Institut de recherche sur l'hydrogene, Quebec, Canada), un carbone avec un plus grand degre de graphitisation et une meilleure porosite. Le Chapitre 1 est une description generale des PEMFCs (PEMFC -- Polymer Electrolyte Membrane Fuel Cell) et plus particulierement des CNS comme support de catalyseurs, leur synthese et purification. Le Chapitre 2 decrit plus en details la methode de synthese et la purification des CNS, la theorie de formation des nanostructures et les differentes techniques de caracterisation que nous avons utilises telles que la diffraction aux rayons-X (XRD -- X-ray diffraction), la microscopie electronique a transmission (TEM -- transmission electron microscope ), la spectroscopie Raman, les isothermes d'adsorption d'azote a 77 K (analyse BET, t-plot, DFT), l'intrusion au mercure, et l'analyse thermogravimetrique (TGA -- thermogravimetric analysis). Le Chapitre 3 presente les resultats obtenus a chaque etape de la synthese des CNS et avec des echantillons produits a l'aide d'un broyeur de type SPEXRTM (SPEX/CertiPrep 8000D) et d'un broyeur de type planetaire (Fritsch Pulverisette 5). La difference essentielle entre ces deux types de broyeur est la facon avec laquelle les materiaux sont broyes. Le broyeur de type SPEX secoue le creuset contenant les materiaux et des billes d'acier selon 3 axes produisant ainsi des impacts de tres grande energie. Le broyeur planetaire quant a lui fait tourner et deplace le creuset contenant les materiaux et des billes d'acier selon 2 axes (plan). Les materiaux sont donc broyes differemment et l'objectif est de voir si les CNS produits ont les memes structures et proprietes. Lors de nos travaux nous avons ete confrontes a un probleme majeur. Nous n'arrivions pas a reproduire les CNS dont la methode de synthese a originellement ete developpee dans les laboratoires de l'Institut de

  7. Development and Characterization of Multilayer Integrated Warhead Structure.

    DTIC Science & Technology

    1985-05-01

    the final concept. Steel castings ( 17 - 4PH ) were made and specimens were machined to characterize the structural properties of the concept. The pioperty...casting 17 - 4PH test specimens and characterizing these composite structures. It was anticipated that problem would occur in the transition . from...MULTILAYER Final Report INTEGRATED WARHEAD STRUCTURE 3/ 17 /83 to 9/30/84 G. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(a) 0. CONTRACT OR GRANT NUMBER(s) D

  8. Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and detailed phylogenetic analysis.

    PubMed

    Mallatt, Jon; Craig, Catherine Waggoner; Yoder, Matthew J

    2012-09-01

    This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ~33 of the ~36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/~jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A-F, or 6A-C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly

  9. Characterization of Vapor Deposited Nano Structured Membranes

    SciTech Connect

    Jankowski, A; Cherepy, N; Ferreira, J; Hayes, J

    2004-03-25

    The vapor deposition methods of planar magnetron sputtering and electron-beam evaporation are used to synthesize materials with nano structured morphological features that have ultra-high surface areas with continuous open porosity at the nano scale. These nano structured membranes are used in a variety of fuel cells to provide electrode and catalytic functions. Specifically, stand alone and composite nickel electrodes for use in thin film solid-oxide, and molten carbonate fuel cells are formed by sputter deposition and electron bean evaporation, respectively. Also, a potentially high-performance catalyst material for the direct reformation of hydrocarbon fuels at low temperatures is deposited as a nano structure by the reactive sputtering of a copper-zinc alloy using a partial pressure of oxygen at an elevated substrate temperature.

  10. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules

    NASA Astrophysics Data System (ADS)

    Noel, Jeffrey K.; Onuchic, José N.

    Structural biology techniques, such as nuclear magnetic resonance (NMR), x-ray crystallography, and cryogenic electron microscopy (cryo-EM), have provided extraordinary insights into the details of the functional configurations of biomolecular systems. Recent advances in x-ray crystallography and cryo-EM have allowed for structural characterization of large molecular machines such as the ribosome, proteasome, and spliceosome. This deluge of structural data has been complemented by experimental techniques capable of probing dynamic information, such as Förster resonance energy transfer (FRET) and stopped flow spectrometry. While these experimental studies have provided tremendous insights into the dynamics of biomolecular systems, it is often difficult to combine the low resolution dynamical data with the high-resolution structural data into a consistent picture. Computer simulation of these biomolecular systems bridges static structural data with dynamic experiments at atomic resolution (Fig. 1).

  11. DNA Microarrays for Aptamer Identification and Structural Characterization

    DTIC Science & Technology

    2012-09-01

    AFRL-RH-WP-TR-2013-0130 DNA MICROARRAYS FOR APTAMER IDENTIFICATION AND STRUCTURAL CHARACTERIZATION Jennifer A. Martin National Research Council...Interim September 2010 to September 2012 4. TITLE AND SUBTITLE DNA Microarrays for Aptamer Identification and Structural Characterization 5a. CONTRACT... Aptamers are ideal recognition elements, but integrating aptamers onto a sensor platform has two main challenges: (1) aptamers are selected in

  12. Spectroscopic and structural characterization of pascoite

    NASA Astrophysics Data System (ADS)

    Reddy, G. Udayabhaskara; Reddy, R. Ramasubba; Reddy, S. Lakshmi; Frost, Ray L.; Endo, Tamio

    2011-09-01

    Pascoite mineral having yellow-orange colour of Colorado, USA origin has been characterized by EPR, optical and NIR spectroscopy. The colour dark red-orange to yellow-orange colour of the pascoite indicates that the mineral contain mixed valency of vanadium. The optical spectrum exhibits a number of electronic bands due to presence of VO(II) ions in the mineral. From EPR studies, the parameters of g, A are evaluated and the data confirm that the ion is in distorted octahedron. Optical absorption studies reveal that two sets of VO(II) is in distorted octahedron. The bands in NIR spectra are due to the overtones and combinations of water molecules.

  13. Structural Characterization of Bacterioferritin from Blastochloris viridis

    PubMed Central

    Wahlgren, Weixiao Y.; Omran, Hadil; von Stetten, David; Royant, Antoine; van der Post, Sjoerd; Katona, Gergely

    2012-01-01

    Iron storage and elimination of toxic ferrous iron are the responsibility of bacterioferritins in bacterial species. Bacterioferritins are capable of oxidizing iron using molecular oxygen and import iron ions into the large central cavity of the protein, where they are stored in a mineralized form. We isolated, crystallized bacterioferritin from the microaerophilic/anaerobic, purple non-sulfur bacterium Blastochloris viridis and determined its amino acid sequence and X-ray structure. The structure and sequence revealed similarity to other purple bacterial species with substantial differences in the pore regions. Static 3- and 4-fold pores do not allow the passage of iron ions even though structural dynamics may assist the iron gating. On the other hand the B-pore is open to water and larger ions in its native state. In order to study the mechanism of iron import, multiple soaking experiments were performed. Upon Fe(II) and urea treatment the ferroxidase site undergoes reorganization as seen in bacterioferritin from Escherichia coli and Pseudomonas aeruginosa. When soaking with Fe(II) only, a closely bound small molecular ligand is observed close to Fe1 and the coordination of Glu94 to Fe2 changes from bidentate to monodentate. DFT calculations indicate that the bound ligand is most likely a water or a hydroxide molecule representing a product complex. On the other hand the different soaking treatments did not modify the conformation of other pore regions. PMID:23056552

  14. Structural and electronic characterisation of π-extended tetrathiafulvalene derivatives as active components in field-effect transistors† †Electronic supplementary information (ESI) available: Experimental procedures, characterization data, XRD single crystal data, computational details and device fabrication. CCDC 1460868 and 1460869. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6ce01200k Click here for additional data file. Click here for additional data file.

    PubMed Central

    Campos, Antonio; Oxtoby, Neil; Galindo, Sergi; Pfattner, Raphael; Veciana, Jaume; Bromley, Stefan T.

    2016-01-01

    The electronic and structural properties of two tetrathiafulvalene derivatives bearing aromatic benzene rings are reported. Thin film transistors of these materials show p-type characteristics with comparable mobility values. It is found that the rigidification of the molecule is beneficial for reducing the reorganisation energy but also has an unfavorable impact on the electronic structure dimensionality. PMID:27774040

  15. Towards detailed knowledge of atomic nuclei—the past, present and future of nuclear structure investigations at GSI

    NASA Astrophysics Data System (ADS)

    Gerl, J.; Gorska, M.; Wollersheim, H. J.

    2016-10-01

    Selected experimental nuclear structure physics results are presented which have been obtained at GSI since the mid 70ties employing the UNILAC and the SIS/FRS accelerator facility. It is shown how stable heavy-ion beams as well as radioactive isotope beams of this facility together with state-of-the-art instrumentation produced many discoveries and led to a multitude of important results covering many aspects of nuclear structure. Finally, we discuss the future directions of nuclear structure research at GSI with the FAIR/NUSTAR project.

  16. An image-based model of the whole human heart with detailed anatomical structure and fiber orientation.

    PubMed

    Deng, Dongdong; Jiao, Peifeng; Ye, Xuesong; Xia, Ling

    2012-01-01

    Many heart anatomy models have been developed to study the electrophysiological properties of the human heart. However, none of them includes the geometry of the whole human heart. In this study, an anatomically detailed mathematical model of the human heart was firstly reconstructed from the computed tomography images. In the reconstructed model, the atria consisted of atrial muscles, sinoatrial node, crista terminalis, pectinate muscles, Bachmann's bundle, intercaval bundles, and limbus of the fossa ovalis. The atrioventricular junction included the atrioventricular node and atrioventricular ring, and the ventricles had ventricular muscles, His bundle, bundle branches, and Purkinje network. The epicardial and endocardial myofiber orientations of the ventricles and one layer of atrial myofiber orientation were then measured. They were calculated using linear interpolation technique and minimum distance algorithm, respectively. To the best of our knowledge, this is the first anatomically-detailed human heart model with corresponding experimentally measured fibers orientation. In addition, the whole heart excitation propagation was simulated using a monodomain model. The simulated normal activation sequence agreed well with the published experimental findings.

  17. Amplification and characterization of eukaryotic structural genes.

    PubMed

    Maniatis, T; Efstratiadis, A; Sim, G K; Kafatos, F

    1978-05-01

    An approach to the study of eukaryotic structural genes which are differentially expressed during development is described. This approach involves the isolation and amplification of mRNA sequences by in vitro conversion of mRNA to double-stranded cDNA followed by molecular cloning in bacterial plasmids. This procedure provides highly specific hybridization probes that can be used to identify genes and their contiguous DNA sequences in genomic DNA, and to detect specific RNA transcripts during development. The nature of the method allows the isolation of individual mRNA sequences from a complex population of molecules at different stages of development.

  18. Characterizing the Community Structure of Complex Networks

    PubMed Central

    Lancichinetti, Andrea; Kivelä, Mikko; Saramäki, Jari; Fortunato, Santo

    2010-01-01

    Background Community structure is one of the key properties of complex networks and plays a crucial role in their topology and function. While an impressive amount of work has been done on the issue of community detection, very little attention has been so far devoted to the investigation of communities in real networks. Methodology/Principal Findings We present a systematic empirical analysis of the statistical properties of communities in large information, communication, technological, biological, and social networks. We find that the mesoscopic organization of networks of the same category is remarkably similar. This is reflected in several characteristics of community structure, which can be used as “fingerprints” of specific network categories. While community size distributions are always broad, certain categories of networks consist mainly of tree-like communities, while others have denser modules. Average path lengths within communities initially grow logarithmically with community size, but the growth saturates or slows down for communities larger than a characteristic size. This behaviour is related to the presence of hubs within communities, whose roles differ across categories. Also the community embeddedness of nodes, measured in terms of the fraction of links within their communities, has a characteristic distribution for each category. Conclusions/Significance Our findings, verified by the use of two fundamentally different community detection methods, allow for a classification of real networks and pave the way to a realistic modelling of networks' evolution. PMID:20711338

  19. Implications of Model Structure and Detail for Utility Planning: Scenario Case Studies Using the Resource Planning Model

    SciTech Connect

    Mai, Trieu; Barrows, Clayton; Lopez, Anthony; Hale, Elaine; Dyson, Mark; Eurek, Kelly

    2015-04-01

    In this report, we analyze the impacts of model configuration and detail in capacity expansion models, computational tools used by utility planners looking to find the least cost option for planning the system and by researchers or policy makers attempting to understand the effects of various policy implementations. The present analysis focuses on the importance of model configurations — particularly those related to capacity credit, dispatch modeling, and transmission modeling — to the construction of scenario futures. Our analysis is primarily directed toward advanced tools used for utility planning and is focused on those impacts that are most relevant to decisions with respect to future renewable capacity deployment. To serve this purpose, we develop and employ the NREL Resource Planning Model to conduct a case study analysis that explores 12 separate capacity expansion scenarios of the Western Interconnection through 2030.

  20. Multiscale Structure of UXO Site Characterization: Spatial Estimation and Uncertainty Quantification

    SciTech Connect

    Ostrouchov, George; Doll, William E.; Beard, Les P.; Morris, Max D.; Wolf, Dennis A

    2009-01-01

    Unexploded ordnance (UXO) site characterization must consider both how the contamination is generated and how we observe that contamination. Within the generation and observation processes, dependence structures can be exploited at multiple scales. We describe a conceptual site characterization process, the dependence structures available at several scales, and consider their statistical estimation aspects. It is evident that most of the statistical methods that are needed to address the estimation problems are known but their application-specific implementation may not be available. We demonstrate estimation at one scale and propose a representation for site contamination intensity that takes full account of uncertainty, is flexible enough to answer regulatory requirements, and is a practical tool for managing detailed spatial site characterization and remediation. The representation is based on point process spatial estimation methods that require modern computational resources for practical application. These methods have provisions for including prior and covariate information.

  1. Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1

    NASA Astrophysics Data System (ADS)

    Kim, Soo-Kyung; Goddard, William A.

    2014-12-01

    Olfactory receptors (ORs) are responsible for mediating the sense of smell; they allow humans to recognize an enormous number of odors but the connection between binding and perception is not known. We predict the ensemble of low energy structures for the human OR1G1 (hOR1G1) and also for six other diverse ORs, using the G protein-coupled receptor Ensemble of Structures in Membrane BiLayer Environment complete sampling method that samples 13 trillion different rotations and tilts using four different templates to predict the 24 structures likely to be important in binding and activation. Our predicted most stable structures of hOR1G1 have a salt-bridge between the conserved D3.49 and K6.30 in the D(E)RY region, that we expect to be associated with an inactive form. The hOR1G1 structure also has specific interaction in transmembrane domains (TMD) 3-6 (E3.39 and H6.40), which is likely an important conformational feature for all hORs because of the 94 to 98 % conservation among all hOR sequences. Of the five ligands studied (nonanal, 9-decen-1-ol, 1-nonanol, camphor, and n-butanal), we find that the 4 expected to bind lead to similar binding energies with nonanol the strongest.

  2. Structural Characterization of Methanol Substituted Lanthanum Halides

    PubMed Central

    Boyle, Timothy J.; Ottley, Leigh Anna M.; Alam, Todd M.; Rodriguez, Mark A.; Yang, Pin; Mcintyre, Sarah K.

    2010-01-01

    The first study into the alcohol solvation of lanthanum halide [LaX3] derivatives as a means to lower the processing temperature for the production of the LaBr3 scintillators was undertaken using methanol (MeOH). Initially the de-hydration of {[La(µ-Br)(H2O)7](Br)2}2 (1) was investigated through the simple room temperature dissolution of 1 in MeOH. The mixed solvate monomeric [La(H2O)7(MeOH)2](Br)3 (2) compound was isolated where the La metal center retains its original 9-coordination through the binding of two additional MeOH solvents but necessitates the transfer of the innersphere Br to the outersphere. In an attempt to in situ dry the reaction mixture of 1 in MeOH over CaH2, crystals of [Ca(MeOH)6](Br)2 (3) were isolated. Compound 1 dissolved in MeOH at reflux temperatures led to the isolation of an unusual arrangement identified as the salt derivative {[LaBr2.75•5.25(MeOH)]+0.25 [LaBr3.25•4.75(MeOH)]−0.25} (4). The fully substituted species was ultimately isolated through the dissolution of dried LaBr3 in MeOH forming the 8-coordinated [LaBr3(MeOH)5] (5) complex. It was determined that the concentration of the crystallization solution directed the structure isolated (4 concentrated; 5 dilute) The other LaX3 derivatives were isolated as [(MeOH)4(Cl)2La(µ-Cl)]2 (6) and [La(MeOH)9](I)3•MeOH (7). Beryllium Dome XRD analysis indicated that the bulk material for 5 appear to have multiple solvated species, 6 is consistent with the single crystal, and 7 was too broad to elucidate structural aspects. Multinuclear NMR (139La) indicated that these compounds do not retain their structure in MeOD. TGA/DTA data revealed that the de-solvation temperatures of the MeOH derivatives 4 – 6 were slightly higher in comparison to their hydrated counterparts. PMID:20514349

  3. Structural characterization of nanowires and nanowire arrays

    NASA Astrophysics Data System (ADS)

    Becker, Catherine Rose

    Nanowires, which have diameter less than a few hundred nanometers and high aspect ratios, may have the same properties as their corresponding bulk materials, or may exhibit unique properties due to their confined dimensions and increased surface to volume ratios. They are a popular field of technological investigation in applications that depend on the transport of charge carriers, because of expectations that microcircuit miniaturization will lead to the next boom in the electronics industry. In this work, the high spatial resolution afforded by transmission electron microscopy (TEM) is used to study nanowires formed by electrochemical deposition into porous alumina templates. The goal is to determine the effect of the synthesis and subsequent processing on the microstructure and crystallinity of the wires. A thorough understanding of the microstructural features of a material is vital for optimizing its performance in a desired application. Two material systems were studied in this work. The first is bismuth telluride (Bi 2Te3), which is used in thermoelectric applications. The second is metallic copper, the electrochemical deposition of which is of interest for interconnects in semiconductor devices. The first part of this work utilized TEM to obtain a thorough characterization of the microstructural features of individual Bi2Te3 nanowires following release from the templates. As deposited, the nanowires are fine grained and exhibit significant lattice strain. Annealing increases the grain size and dislocations are created to accommodate the lattice strain. The degree of these microstructural changes depends on the thermal treatment. However, no differences were seen in the nanowire microstructure as a function of the synthetic parameters. The second part of this work utilized a modified dark field TEM technique in order to obtain a spatially resolved, semi-quantitative understanding of the evolution of preferred orientation as a function of the electrochemical

  4. Characterization of Fine Structure in Sprites

    NASA Astrophysics Data System (ADS)

    Gerken, E. A.; Inan, U. S.

    2001-12-01

    During the summer months of 1998-2000, Stanford University fielded campaigns to telescopically image sprites. The campaigns were conducted at Langmuir Laboratory (operated by New Mexico Institute of Mining and Technology) in Socorro NM and Yucca Ridge Observatory in Fort Collins CO. The experiment consisted of two intensified CCD cameras, two photometers, and crossed magnetic loop VLF antennas. One camera was mounted on a 16in diameter, 72in focal length Newtonian telescope with a field of view of 0.72x0.9 degrees and the other had a 50mm lens with a field of view of 9x12 degrees. Similarly one photometer was mounted on an 8in diameter, 1200mm focal length Newtonian telescope with a circular field of view of 1 degree and the second was red-filtered and had a wider field of view of 3x6 degrees. All four instruments were mounted on the same platform and were aligned. Video data was stored on VHS tapes with the photometer signals recorded on the audio channels. GPS video time-stamping and IRIG-B code were used for timing. Data from these campaigns reveal streamer structures within sprites ranging from 25m to 200m in width. Streamer morphologies are diverse ranging from single columns to multiply-forked structures to chains of beads. Faint downward branching is observed prior to some large sprite events. Streamers are seen to develop on time scales from less than 17ms to over 100ms. Streamer sizes and velocities are compared to existing models and charge moments for associated sferics are presented.

  5. 10. DETAIL, CAB SIDE. DETAIL, END OF BOOM. DETAIL, LOWER ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. DETAIL, CAB SIDE. DETAIL, END OF BOOM. DETAIL, LOWER PART OF TOWER, SHOWING METAL WHEELS AND CABLE SPOOLS. DETAIL, LOOKING UP AT THE UNDERSIDE OF THE REVOLVING PLATFORM ATOP THE TOWER. - United Engineering Company Shipyard, Crane, 2900 Main Street, Alameda, Alameda County, CA

  6. Nickel(II), copper(II) and zinc(II) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation.

    PubMed

    Lauria, Antonino; Bonsignore, Riccardo; Terenzi, Alessio; Spinello, Angelo; Giannici, Francesco; Longo, Alessandro; Almerico, Anna Maria; Barone, Giampaolo

    2014-04-28

    We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-dC)]2 and [poly(dA-dT)]2. Structural details of the intercalation site of the three metal complexes within [dodeca(dA-dT)]2 were obtained by molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations. The calculations revealed that three major intermolecular interactions contribute to the strong affinity between DNA and the three metal complexes: (1) the electrostatic attraction between the two positively charged triethylammoniummethyl groups of the metal complexes and the negatively charged phosphate groups of the DNA backbone; (2) the intercalation of the naphthalene moiety within the four nitrogen bases of the intercalation site; (3) the metal coordination by exocyclic donor atoms of the bases, specifically the carbonyl oxygen and amine nitrogen atoms. Remarkably, the Gibbs formation free energy calculated for the intercalation complexes of 1, 2 and 3 with [dodeca(dA-dT)]2 in the implicit water solution is in agreement with the experimental Gibbs free energy values obtained from the DNA-binding constants as ΔG° = -RT ln(K(b)). In particular, the DNA-binding affinity trend, 1 > 2 > 3, is reproduced. Finally, the first shell coordination distances calculated for the intercalation complex 3/[dodeca(dA-dT)]2 are in

  7. Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.

    PubMed

    Thirup, Søren S; Van, Lan Bich; Nielsen, Tine K; Knudsen, Charlotte R

    2015-07-01

    Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks. Often, guanine-nucleotide exchange factors are essential to this process. During translation, EF-Tu:GTP transports aminoacylated tRNA to the ribosome. GTP is hydrolyzed during this process, and subsequent reactivation of EF-Tu is catalyzed by EF-Ts. The reaction path of guanine-nucleotide exchange is structurally poorly defined for EF-Tu and EF-Ts. We have determined the crystal structures of the following reaction intermediates: two structures of EF-Tu:GDP:EF-Ts (2.2 and 1.8Å resolution), EF-Tu:PO4:EF-Ts (1.9Å resolution), EF-Tu:GDPNP:EF-Ts (2.2Å resolution) and EF-Tu:GDPNP:pulvomycin:Mg(2+):EF-Ts (3.5Å resolution). These structures provide snapshots throughout the entire exchange reaction and suggest a mechanism for the release of EF-Tu in its GTP conformation. An inferred sequence of events during the exchange reaction is presented.

  8. Structure and characterization of AAT-1 isoforms.

    PubMed

    Matsuda, Eiko; Ishizaki, Ray; Taira, Takahiro; Iguchi-Ariga, Sanae M M; Ariga, Hiroyoshi

    2005-05-01

    A novel protein, AAT-1, was identified as a AMY-1-binding protein and three splicing variants of AAT-1, AAT-1alpha, -beta and -gamma were identified. The function of AAT-1 is thought to be related to spermatogenesis. In this study, we further identified other splicing isoforms of AAT-1, AAT-1L, AAT-1M and AAT-1S, consisting of 767, 603 and 252 amino acids, respectively. These isoforms were found to use a promoter different from that used by AAT-1alpha, -beta and -gamma in the aat-1 gene, which contains 20 exons. Only 60 amino acids in the C-terminal portion of AAT-1 derived from exons 15-17 are common among AAT-1L, AAT-1M, AAT-1S and AAT-1alpha. While AAT-1alpha is specifically expressed in the testis, AAT-1L, AAT-1M, AAT-1S were found to be differentially expressed in human tissues. All of the isoforms of AAT-1 were found to bind to and colocalized with AMY-1 in human cells. While AAT-1L and AAT-1M were found to be localized diffusely in the cytoplasm, AAT-1S, like AAT-1alpha, was found to be localized in the mitochondria-like structure, suggesting different roles of AAT-1 isoforms in cells.

  9. Structural characterization of MAPLE deposited lipase biofilm

    NASA Astrophysics Data System (ADS)

    Aronne, Antonio; Ausanio, Giovanni; Bloisi, Francesco; Calabria, Raffaela; Califano, Valeria; Fanelli, Esther; Massoli, Patrizio; Vicari, Luciano R. M.

    2014-11-01

    Lipases (triacylglycerol ester hydrolases) are enzymes used in several industrial applications. Enzymes immobilization can be used to address key issues limiting widespread application at industrial level. Immobilization efficiency is related to the ability to preserve the native conformation of the enzyme. MAPLE (Matrix Assisted Pulsed Laser Evaporation) technique, a laser deposition procedure for treating organic/polymeric/biomaterials, was applied for the deposition of lipase enzyme in an ice matrix, using near infrared laser radiation. Microscopy analysis showed that the deposition occurred in micrometric and submicrometric clusters with a wide size distribution. AFM imaging showed that inter-cluster regions are uniformly covered with smaller aggregates of nanometric size. Fourier transform infrared spectroscopy was used for both recognizing the deposited material and analyzing its secondary structure. Results showed that the protein underwent reversible self-association during the deposition process. Actually, preliminary tests of MAPLE deposited lipase used for soybean oil transesterification with isopropyl alcohol followed by gas chromatography-mass spectrometry gave results consistent with undamaged deposition of lipase.

  10. Aromatase inhibitors: structural features and biochemical characterization.

    PubMed

    Hong, Yanyan; Chen, Shiuan

    2006-11-01

    Aromatase is the enzyme synthesizing estrogens from androgens. In estrogen-dependent breast tumors, estrogens induce the expression of growth factors responsible for cancer cell proliferation. In situ estrogen synthesis by aromatase "is thought to play a key role in the promotion of breast cancer growth. Aromatase inhibitors (AIs) provide new approaches for the prevention and treatment of breast cancer by inhibiting estrogen biosynthesis. Through reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemical techniques, aromatase has been found to be expressed in many endocrine tissues and tumors originating from these tissues. Unexpectedly, this enzyme is now known to also be expressed in liver, lung, and colon cancers. Such findings suggest a potential role for endocrine manipulation of these types of cancer using AIs. Three Food and Drug Administration (FDA)-approved AIs, anastrozole (Arimidex), letrozole (Femara), and exemestane (Aromasin), effectively challenging tamoxifen, have been used as first-line drugs in the treatment of hormone-dependent breast cancer, and possibly other aromatase-expressing cancers. In addition, natural anti-aromatase chemicals, such as flavones and coumarins, have been identified. Efforts to develop new lines of AIs derived from these phytochemicals have been initiated in several laboratories. Finally, significant progress has been made in the understanding of the structure-function relationship of aromatase. Such information has helped the examination of binding characteristics of AIs, the evaluation of reaction mechanism of aromatase, and the explanation of the molecular basis for a low catalytic activity of the natural variant, M364T.

  11. Detailed structural study of β-artemether: Density functional theory (DFT) calculations of Infrared, Raman spectroscopy, and vibrational circular dichroism

    NASA Astrophysics Data System (ADS)

    Wang, Zhiqiang; Chen, Jianchao; Li, Linwei; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2015-10-01

    In this study, the experimental and theoretical studies on the structure of β-artemether are presented. The optimized molecular structure, Mulliken atomic charges, vibrational spectra (IR, Raman and vibrational circular dichroism), and molecular electrostatic potential have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (2d, p) basis set. Reliable vibrational assignments for Artemether have been made on the basis of potential energy distribution (PED). The vibrational circular dichroism (VCD) has been explored by ab initio calculations, and then was used to compare with the experimental VCD. The consistence between them confirmed the absolute configuration of Artemether. In addition, HOMO-LUMO of the title compound as well as thermo-dynamical parameters has illustrated the stability of β-artemether.

  12. SMS crew station (C and D panels and forward structures). CEI part 1: Detail specification, type 1 data

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Established are the requirements for performance, design, test and qualification of one type of equipment identified as SMS C&D panels and forward structures. This CEI is used to provide all hardware and wiring necessary for the C&D panels to be properly interfaced with the computer complex/signal conversion equipment (SCE), crew station, and software requirements as defined in other CEI specifications.

  13. Surface characterization of semiconductor photocathode structures

    NASA Astrophysics Data System (ADS)

    Liu, Zhi

    The need for a high performance photocathode in the electron beam lithography and microscopy is well established. Previous research demonstrated high brightness (1 x 108 A/cm2-sr at 3 KeV), and an energy spread as low as 50meV at room temperature for a GaAs based negative electron affinity (NEA) cathode in a sealed-off tube. However the GaAs cathodes suffer rapid decay in an open vacuum system. Achieving a clean, stoichiometric and repeatable GaAs(100) surface was the first step in this study. Based on the knowledge obtained from synchrotron radiation photoelectron spectroscopy, we successfully developed and optimized a reliable surface cleaning technique for our GaAs photocathodes. The fully activated photocathode and its decay under different vacuum conditions were investigated. The NEA activation layer is about 1 nm thick and was very vulnerable to oxygen in the system. A revised double dipole structural model was proposed to explain how the Cs/O co-deposition could produce a NEA surface. We found the chemical changes of oxygen species in the activation layer caused the initial quantum yield (QY) decay of the cathode. Further exposure to oxygen oxidized the substrate and permanently reduced the QY to zero. Energy distribution curve measurements of GaAs(100) and GaN(0001) NEA surfaces were performed under laser illumination. We found that the main contribution to the total emitted current of NEA GaAs and GaN surfaces was due to the electrons that were lost an average 140meV and 310 meV respectively in the near surface region prior to emission into vacuum. This energy loss is due not to the scattering through Cs or Cs/O layer; In GaN, it is probably due to a Gunn-like effect involving inter-valley phonon scattering within the band-bending region. We observed a highly directional emission profile from GaAs cathodes (electrons emitted within a semi-angle of 15° relative to the surface normal). In practice, it is expected that the highly directional photoemission

  14. Geophysical characterization of the Chicxulub impact structure

    NASA Astrophysics Data System (ADS)

    Gulick, S. P.; Christeson, G. L.; Barton, P. J.; Grieve, R. A.; Morgan, J. V.; Fucugauchi, J. U.

    2013-05-01

    The Chicxulub impact structure, conclusively linked to the 65.5 Ma mass extinction, includes three sets of inward dipping, ring faults, between 70 and 130 km radially with a topographically elevated inner rim, at the inner edge of these faults except in the northeast where such a rim is absent. Slump blocks offset by large faults result in a terrace zone, that steps down from the inner rim into the annular trough. The inner blocks underlie the peak ring --an internal topographic ring of topography that exhibits variable relief due to target asymmetries and bounds the coherent melt sheet within the central basin. Impact breccias lie within the annular trough above the slump blocks and proximal ejecta and within the central basin above the melt sheet. Beneath the melt sheet is the top of the central uplift, displaced by >10 km vertically, and an upwarped Moho, displaced by 1-2 km. These interpretations and hydrocode models support the following working hypothesis for the formation of Chicxulub: a 50 km radius transient cavity, lined with melt and impact breccia, formed within 10s of seconds of the 65.5 Ma impact and within minutes, weakened rebounding crust rose above kilometers above the surface, the transient crater rim underwent localized, brittle deformation and collapsed into large slump blocks resulting in a inner rim being preserved 70-85 km from crater center, and ring faults forming farther outwards. The overheightened central uplift of weakened crust collapsed outwards forming the peak ring, and buried the inner slump blocks. Most impact melt that lined the transient cavity was transported on top of the central uplift, ultimately emplaced as a coherent <3-km thick melt sheet that shallows within the inner regions of the peak ring. Smaller pockets of melt flowed into the annular trough. During and likely for sometime after these events, slope collapse, proximal ejecta, ground surge, and tsunami waves infilled the annular trough with sediments up to 3 km

  15. Characterization and Prediction of Protein Flexibility Based on Structural Alphabets

    PubMed Central

    Liu, Bin

    2016-01-01

    Motivation. To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities. Results. In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet. Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter), and the DW structure alphabet (28-letter), are investigated. The conformational entropy is then calculated from the structure alphabet letters. Some of the proteins show high correlation between the conformation entropy and the protein flexibility. We then predict the protein flexibility from basic amino acid sequence. The local structures are predicted by the dual-layer model and the conformational entropy of the predicted class distribution is then calculated. The results show that the conformational entropy is a good indicator of the protein flexibility, but false positives remain a problem. The DW structure alphabet performs the best, which means that more subtle local structures can be captured by large number of structure alphabet letters. Overall this study provides a simple and efficient method for the characterization and prediction of the protein flexibility. PMID:27660756

  16. Micro- and nano-structural details of a spider's filter for substrate vibrations: relevance for low-frequency signal transmission

    PubMed Central

    Erko, Maxim; Younes-Metzler, Osnat; Rack, Alexander; Zaslansky, Paul; Young, Seth L.; Milliron, Garrett; Chyasnavichyus, Marius; Barth, Friedrich G.; Fratzl, Peter; Tsukruk, Vladimir; Zlotnikov, Igor; Politi, Yael

    2015-01-01

    The metatarsal lyriform organ of the Central American wandering spider Cupiennius salei is its most sensitive vibration detector. It is able to sense a wide range of vibration stimuli over four orders of magnitude in frequency between at least as low as 0.1 Hz and several kilohertz. Transmission of the vibrations to the slit organ is controlled by a cuticular pad in front of it. While the mechanism of high-frequency stimulus transfer (above ca 40 Hz) is well understood and related to the viscoelastic properties of the pad's epicuticle, it is not yet clear how low-frequency stimuli (less than 40 Hz) are transmitted. Here, we study how the pad material affects the pad's mechanical properties and thus its role in the transfer of the stimulus, using a variety of experimental techniques, such as X-ray micro-computed tomography for three-dimensional imaging, X-ray scattering for structural analysis, and atomic force microscopy and scanning electron microscopy for surface imaging. The mechanical properties were investigated using scanning acoustic microscopy and nanoindentation. We show that large tarsal deflections cause large deformation in the distal highly hydrated part of the pad. Beyond this region, a sclerotized region serves as a supporting frame which resists the deformation and is displaced to push against the slits, with displacement values considerably scaled down to only a few micrometres. Unravelling the structural arrangement in such specialized structures may provide conceptual ideas for the design of new materials capable of controlling a technical sensor's specificity and selectivity, which is so typical of biological sensors. PMID:25631567

  17. Structural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation

    PubMed Central

    Le, Oanh Thi Tu; Lee, Sang Yoon; Yang, Jin Kuk

    2016-01-01

    The hexameric ATPase p97 has been implicated in diverse cellular processes through interactions with many different adaptor proteins at its N-terminal domain. Among these, the Ufd1-Npl4 heterodimer is a major adaptor, and the p97-Ufd1-Npl4 complex plays an essential role in endoplasmic reticulum-associated degradation (ERAD), acting as a segregase that translocates the ubiquitinated client protein from the ER membrane into the cytosol for proteasomal degradation. We determined the crystal structure of the complex of the N-terminal domain of p97 and the SHP box of Ufd1 at a resolution of 1.55 Å. The 11-residue-long SHP box of Ufd1 binds at the far-most side of the Nc lobe of the p97 N domain primarily through hydrophobic interactions, such that F225, F228, N233 and L235 of the SHP box contact hydrophobic residues on the surface of the p97 Nc lobe. Mutating these key interface residues abolished the interactions in two different binding experiments, isothermal titration calorimetry and co-immunoprecipitation. Furthermore, cycloheximide chase assays showed that these same mutations caused accumulation of tyrosinase-C89R, a well-known ERAD substrate, thus implying decreased rate of protein degradation due to their defects in ERAD function. Together, these results provide structural and biochemical insights into the interaction between p97 N domain and Ufd1 SHP box. PMID:27684549

  18. Characterizing accuracy of total hemoglobin recovery using contrast-detail analysis in 3D image-guided near infrared spectroscopy with the boundary element method

    PubMed Central

    Ghadyani, Hamid R.; Srinivasan, Subhadra; Pogue, Brian W.; Paulsen, Keith D.

    2010-01-01

    The quantification of total hemoglobin concentration (HbT) obtained from multi-modality image-guided near infrared spectroscopy (IG-NIRS) was characterized using the boundary element method (BEM) for 3D image reconstruction. Multi-modality IG-NIRS systems use a priori information to guide the reconstruction process. While this has been shown to improve resolution, the effect on quantitative accuracy is unclear. Here, through systematic contrast-detail analysis, the fidelity of IG-NIRS in quantifying HbT was examined using 3D simulations. These simulations show that HbT could be recovered for medium sized (20mm in 100mm total diameter) spherical inclusions with an average error of 15%, for the physiologically relevant situation of 2:1 or higher contrast between background and inclusion. Using partial 3D volume meshes to reduce the ill-posed nature of the image reconstruction, inclusions as small as 14mm could be accurately quantified with less than 15% error, for contrasts of 1.5 or higher. This suggests that 3D IG-NIRS provides quantitatively accurate results for sizes seen early in treatment cycle of patients undergoing neoadjuvant chemotherapy when the tumors are larger than 30mm. PMID:20720975

  19. Detailed petrophysical characterization enhances geological mapping of a buried substratum using aeromagnetic and gravity data; application to the southwestern Paris basin

    NASA Astrophysics Data System (ADS)

    Baptiste, Julien; Martelet, Guillaume; Faure, Michel; Beccaletto, Laurent; Chen, Yan; Reninger, Pierre-Alexandre

    2016-04-01

    Mapping the geometries (structure and lithology) of a buried basement is a key for targeting resources and for improving the regional geological knowledge. The Paris basin is a Mesozoic to Cenozoic intraplate basin set up on a Variscan substratum, which crops out in the surrounding massifs. We focus our study on the southwestern part of the Paris basin at its junction with the Aquitaine basin. This Mezo-Cenozoic cover separates the Armorican Massif and the Massif Central which compose of several litho-tectonic units bounded by crustal-scale shear zones. In spite of several lithological and structural correlations between various domains of the two massifs, their geological connection, hidden below the Paris basin sedimentary cover, is still largely debated. Potential field geophysics have proven effective for mapping buried basin/basement interfaces. In order to enhance the cartographic interpretation of these data, we have set up a detailed petrophysical library (field magnetic susceptibility data and density measurements on rock samples) of the Paleozoic rocks outcropping in the Variscan massifs. The combination of aeromagnetic and gravity data supported by the petrophysical signatures and field/borehole geological information, is carried out to propose a new map of the architecture of the Variscan substratum. The new synthetic map of geophysical signature of the Paris basin basement combines: i) the magnetic anomaly reduced to the pole, ii) the vertical gradient of the Bouguer anomaly and iii) the tilt derivative of the magnetic anomaly reduced to the pole. Based on this information, the Eastern extension of the major shear zones below the sedimentary cover is assessed. The petrophysical signatures were classified in three classes of magnetic susceptibility and density: low, intermediate and high. Basic rocks have high magnetization and density values whereas granite, migmatite and orthogneiss show low magnetization and density values, Proterozoic and Paleozoic

  20. The characterization of widespread fatigue damage in fuselage structure

    NASA Technical Reports Server (NTRS)

    Piascik, Robert S.; Willard, Scott A.; Miller, Matthew

    1994-01-01

    The characteristics of widespread fatigue damage (WSFD) in fuselage riveted structure were established by detailed nondestructive and destructive examinations of fatigue damage contained in a full size fuselage test article. The objectives of this were to establish an experimental data base for validating emerging WSFD analytical prediction methodology and to identify first order effects that contribute to fatigue crack initiation and growth. Detailed examinations were performed on a test panel containing four bays of a riveted lap splice joint. The panel was removed from a full scale fuselage test article after receiving 60,000 full pressurization cycles. The results of in situ examinations document the progression of fuselage skin fatigue crack growth through crack linkup. Detailed tear down examinations and fractography of the lap splice joint region revealed fatigue crack initiation sites, crack morphology, and crack linkup geometry. From this large data base, distributions of crack size and locations are presented and discussions of operative damage mechanisms are offered.

  1. Structural Characterization of the Novel and Thermal Stable Hydrogenases from the Purple Sulfur Bacteria Thiocapsa Roseopersicina and Lamprobacter Modestohalophilus

    DTIC Science & Technology

    2011-08-01

    fall into three main classes: [NiFe]-, [ FeFe ] and [Fe]- hydrogenases. [NiFe] – hydrogenases are represented in details as the most numerous class...of the effects of coupling model light harvesting complexes to both [NiFe]- and [ FeFe ]-hydrogenases that are the targets of our studies and in...Technical Report Page 20 / 20 characterization are the 1) [ FeFe ]-hydrogenase from Chlamydomonous reinhardtii and 2) the structural characterization of

  2. Synthesis, spectroscopic characterizations, crystal structures and DFT studies of nalidixic acid carbonyl hydrazones derivatives

    NASA Astrophysics Data System (ADS)

    Bergamini, F. R. G.; Ribeiro, M. A.; Lancellotti, M.; Machado, D.; Miranda, P. C. M. L.; Cuin, A.; Formiga, A. L. B.; Corbi, P. P.

    2016-09-01

    This article describes the synthesis and characterization of the 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide (hzd) and six carbonyl hydrazones derivatives of the nalidixic with 1H-pyrrol-2-ylmethylidene (hpyrr), 1H-imidazol-2-ylmethylidene (h2imi), pyridin-2-ylmethylidene (h2py), pyridin-3-ylmethylidene (h3py), pyridin-4-ylmethylidene(h4py) and (2-hydroxyphenyl)methylidene (hsali). The carbonyl hydrazones were characterized by elemental and ESI-QTOF-MS analyses, IR and detailed NMR spectroscopic measurements. The 2D NMR experiments allowed the unambiguous assignment of the hydrogen, carbon and nitrogen atoms, which have not been reported for nalidixic acid carbonyl hydrazone derivatives so far. Crystal structures of hzd and the new carbonyl hydrazones h2imi, hpyrr and h3py were determined by X-ray diffraction studies. Although the synthesis of hzd was reported decades ago, the hzd crystal structure have not been reported yet. Geometric optimizations of all the characterized structures were performed with the aid of DFT studies. Despite the fact that the hydrazones with 2-pyridine carboxylic acid (h2py) and salicyl aldehyde (hsali) were already reported by literature, a detailed spectroscopic study followed by DFT studies are also reported for such compounds in this manuscript. Antimicrobial studies of the compounds are also presented.

  3. Mass Spectrometry Combinations for Structural Characterization of Sulfated-Steroid Metabolites

    NASA Astrophysics Data System (ADS)

    Yan, Yuetian; Rempel, Don L.; Holy, Timothy E.; Gross, Michael L.

    2014-05-01

    Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MSn), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular.

  4. Mathematical model for characterizing noise transmission into finite cylindrical structures

    NASA Astrophysics Data System (ADS)

    Li, Deyu; Vipperman, Jeffrey S.

    2005-02-01

    This work presents a theoretical study of the sound transmission into a finite cylinder under coupled structural and acoustic vibration. Particular attention of this study is focused on evaluating a dimensionless quantity, ``noise reduction,'' for characterizing noise transmission into a small cylindrical enclosure. An analytical expression of the exterior sound pressure resulting from an oblique plane wave impinging upon the cylindrical shell is first presented, which is approximated from the exterior sound pressure for an infinite cylindrical structure. Next, the analytical solution of the interior sound pressure is computed using modal-interaction theory for the coupled structural acoustic system. These results are then used to derive the analytical formula for the noise reduction. Finally, the model is used to predict and characterize the sound transmission into a ChamberCore cylindrical structure, and the results are compared with experimental data. The effects of incidence angle and internal acoustic damping on the sound transmission into the cylinder are also parametrically studied. .

  5. The GEISEIR Cruise: Detailed Investigation of the Southeast Indian Ridge Seeking for a Geochemical Scan of the Upper Mantle Structure

    NASA Astrophysics Data System (ADS)

    Hemond, C.; Albarede, F.

    2008-12-01

    Isotopic heterogeneities along mid-ocean ridges reflect the dynamics of the underlying mantle. Present studies on the Mid Atlantic Ridge obtained on a 50 km step sampling (nearly 500 isotopic analyses of Pb, Nd, Hf and Sr) have revealed that they are dominated by a range of wavelengths between 600 and 5 000 km, which we interpret as reflecting the stretching and refolding of ancient lithospheric plates by mantle convection. It is time to go back to the ridges to deepen our knowledge of the fine mantle source structure underneath them. Graham and Lyon coworkers (2006) recently discovered that, along the South-East Indian Ridge (SEIR), Hf isotope compositions of MORB toggle over some 3000 km between two groups of values separated by a prominent gap. We interpret this pattern as reflecting the presence of striations between isotopically distinct mantle sources. The cumulated number of "toggles" is proportional to the distance along the ridge, which demonstrates the Poissonian character of the striation occurrences (random mixing). This GEISEIR cruise aims at further exploring the hypothesis that the unique isotopic patterns observed along the SEIR reveal striations between ancient mantle sources and recycled material. The isotopic analysis of the 150 samples recovered by the cruises Boomerang 6 and Westward 10 between St Paul and the Australia- Antarctica Discordance is completed. We consider, however, that the present sampling (roughly at a 50 km step) is too crude for an efficient spectral analysis of the data set. In order to improve this, the GEISEIR cruise will allow us to fill up a few existing gaps at 50 km intervals between 82 et 89° E but also to sample the ridge with a step of 10 km between 89° et 96° E and a step of 5 km between 96 and 99° E. This will allow us to obtain statistical distributions for isotope compositions and to assess the effect of sample density by a local decimation of the data. This cruise is scheduled for January-February 2009 on

  6. A new method for the characterization of micro-/nano-periodic structures based on microscopic Moiré fringes.

    PubMed

    Wu, Dan; Xie, Huimin; Tang, Minjin; Hu, Zhenxing

    2014-01-01

    Linewidth and opening ratio (ratio of linewidth to period) are important parameters in characterizing micro-/nano-periodic and quasi-periodic structures. Periodic structures are conventionally characterized by the direct observation of specimens under a microscope. However, the field of view is relatively small, and only certain details can be acquired under a microscope. Moreover, the non-uniformity of the linewidth in quasi-periodic structures cannot be detected. This paper proposes a new characterization method for determining the linewidth and opening ratio of periodic structures based on Moiré fringe analysis. This method has the advantage of full-field characterization of the linewidth of micro-/nano-structures over a larger area than that afforded by direct observation. To validate the method, the linewidth of scanning electron microscope (SEM) scan lines was first calibrated with a standard grating. Next, a microperiodic structure with known geometry was characterized using this calibrated SEM system. The results indicate that the proposed method is simple and effective, indicating a potential approach for the characterization of gratings over large areas. This technique can be extended to various high-power scanning microscopes to characterize micro-/nano-structures.

  7. Characterization of an In Vitro Differentiation Assay for Pancreatic-Like Cell Development from Murine Embryonic Stem Cells: Detailed Gene Expression Analysis

    PubMed Central

    Chen, Chialin; Chai, Jing; Singh, Lipi; Kuo, Ching-Ying; Jin, Liang; Feng, Tao; Marzano, Scott; Galeni, Sheetal; Zhang, Nan; Iacovino, Michelina; Qin, Lihui; Hara, Manami; Stein, Roland; Bromberg, Jonathan S.; Kyba, Michael

    2011-01-01

    Abstract Embryonic stem (ES) cell technology may serve as a platform for the discovery of drugs to treat diseases such as diabetes. However, because of difficulties in establishing reliable ES cell differentiation methods and in creating cost-effective plating conditions for the high-throughput format, screening for molecules that regulate pancreatic beta cells and their immediate progenitors has been limited. A relatively simple and inexpensive differentiation protocol that allows efficient generation of insulin-expressing cells from murine ES cells was previously established in our laboratories. In this report, this system is characterized in greater detail to map developmental cell stages for future screening experiments. Our results show that sequential activation of multiple gene markers for undifferentiated ES cells, epiblast, definitive endoderm, foregut, and pancreatic lineages was found to follow the sequence of events that mimics pancreatic ontogeny. Cells that expressed enhanced green fluorescent protein, driven by pancreatic and duodenal homeobox 1 or insulin 1 promoter, correctly expressed known beta cell lineage markers. Overexpression of Sox17, an endoderm fate-determining transcription factor, at a very early stage of differentiation (days 2–3) enhanced pancreatic gene expression. Overexpression of neurogenin3, an endocrine progenitor cell marker, induced glucagon expression at stages when pancreatic and duodenal homeobox 1 message was present (days 10–16). Forced expression (between days 16 and 25) of MafA, a pancreatic maturation factor, resulted in enhanced expression of insulin genes, glucose transporter 2 and glucokinase, and glucose-responsive insulin secretion. Day 20 cells implanted in vivo resulted in pancreatic-like cells. Together, our differentiation assay recapitulates the proceedings and behaviors of pancreatic development and will be valuable for future screening of beta cell effectors. PMID:21395400

  8. Detailed functional characterization of glycosylated and nonglycosylated variants of malaria vaccine candidate PfAMA1 produced in Nicotiana benthamiana and analysis of growth inhibitory responses in rabbits.

    PubMed

    Boes, Alexander; Spiegel, Holger; Edgue, Gueven; Kapelski, Stephanie; Scheuermayer, Matthias; Fendel, Rolf; Remarque, Edmond; Altmann, Friedrich; Maresch, Daniel; Reimann, Andreas; Pradel, Gabriele; Schillberg, Stefan; Fischer, Rainer

    2015-02-01

    One of the most promising malaria vaccine candidate antigens is the Plasmodium falciparum apical membrane antigen 1 (PfAMA1). Several studies have shown that this blood-stage antigen can induce strong parasite growth inhibitory antibody responses. PfAMA1 contains up to six recognition sites for N-linked glycosylation, a post-translational modification that is absent in P. falciparum. To prevent any potential negative impact of N-glycosylation, the recognition sites have been knocked out in most PfAMA1 variants expressed in eukaryotic hosts. However, N-linked glycosylation may increase efficacy by improving immunogenicity and/or focusing the response towards relevant epitopes by glycan masking. We describe the production of glycosylated and nonglycosylated PfAMA1 in Nicotiana benthamiana and its detailed characterization in terms of yield, integrity and protective efficacy. Both PfAMA1 variants accumulated to high levels (>510 μg/g fresh leaf weight) after transient expression, and high-mannose-type N-glycans were confirmed for the glycosylated variant. No significant differences between the N. benthamiana and Pichia pastoris PfAMA1 variants were detected in conformation-sensitive ligand-binding studies. Specific titres of >2 × 10(6) were induced in rabbits, and strong reactivity with P. falciparum schizonts was observed in immunofluorescence assays, as well as up to 100% parasite growth inhibition for both variants, with IC₅₀ values of ~35 μg/mL. Competition assays indicated that a number of epitopes were shielded from immune recognition by N-glycans, warranting further studies to determine how glycosylation can be used for the directed targeting of immune responses. These results highlight the potential of plant transient expression systems as a production platform for vaccine candidates.

  9. Characterizing Thematized Derivative Schema by the Underlying Emergent Structures

    ERIC Educational Resources Information Center

    Garcia, Mercedes; Llinares, Salvador; Sanchez-Matamoros, Gloria

    2011-01-01

    This paper reports on different underlying structures of the derivative schema of three undergraduate students that were considered to be at the trans level of development of the derivative schema (action-process-object-schema). The derivative schema is characterized in terms of the students' ability to explicitly transfer the relationship between…

  10. Faculty Perceptions of Students: Structure of Faculty Characterizations, Part III.

    ERIC Educational Resources Information Center

    Davis, Junius A.

    The structure of characterizations of college students by faculty members, particularly observable and significant dimensions or trait patterns, were investigated. Student ratings by faculty members on 80 bi-polar traits, together with Scholastic Aptitude Test (SAT) scores and high school and college freshman average grades, were obtained.…

  11. Preliminary Characterization and Classification Scheme for Tectonic Structures on Enceladus

    NASA Astrophysics Data System (ADS)

    Nahm, A.; Kattenhorn, S. A.

    2013-12-01

    The ice shell of Enceladus has experienced widespread and diverse tectonic deformation. Its leading and trailing hemispheres are pervasively fractured and these are separated by older cratered terrains on the sub- and anti-Saturnian hemispheres that exhibit relatively little tectonic deformation. The south polar terrain (SPT) is tectonically complex, geologically active, and is separated from the rest of Enceladus by the south polar dichotomy. The diversity of structures visible on the surface attests to a complicated and perhaps long-lived tectonic history. Currently, no fundamental classification scheme based on formation mechanisms exists for the tectonic structures on Enceladus, as does for Europa, which limits analysis and discussion of tectonic structures and the regional and global tectonic history. Characterization and classification of structures based on their formation mechanisms allows for the stress states (orientation, magnitude, and sense) responsible for their formation to be inferred. Thus, characterizing and classifying structures on Enceladus is a major first step in understanding its tectonic history. Here, we present a preliminary global classification scheme for tectonic structures on Enceladus. The basemap used for our preliminary structure classification was the global Imaging Science Subsystem (ISS) mosaic obtained from Ciclops (110 mpp; http://www.ciclops.org/view/7590/Map_of_Enceladus_-_December_2011?js=1). The structures observed on the surface have been divided into fifteen classes based on morphology. These classes represent the diversity of structure morphology on Enceladus and include the 'tiger stripes' in the SPT, the arcuate ridges that make up the south polar dichotomy, wide fracture complexes, several classes of narrow fractures, curvilinear subparallel fractures, rifts that extend north from the SPT boundary, terrain reminiscent of Ganymede's grooved terrain, and topographic ridges with multiple orientations. The preliminary

  12. Structural characterization of Zn-In-Se thin films

    NASA Astrophysics Data System (ADS)

    Güllü, H. H.; Parlak, M.

    2017-02-01

    In this study, structural properties of the Zn-In-Se (ZIS) thin films deposited by thermal evaporation method were investigated. The as-grown and annealed ZIS films were found in polycrystalline structure with the main orientation in (112) direction. The compositional analysis of the films showed that they were in Zn-rich behavior and there was a slight change in the elemental contribution to the structure with annealing process. Raman analysis was carried out to determine the crystalline structure and the different vibration modes of ZIS thin films. According to these measurements, the highest Raman intensity was in the LO mode which was directly proportional to the crystallinity of the samples. The atomic force microscopy (AFM) analyses were done in order to obtain detailed information about the morphology of the thin film surface. The surface of the films was observed as nearly-smooth and uniform in as-grown and annealed forms. X-ray photoelectron spectroscopy (XPS) measurements were analyzed to get detailed information about surface and near-surface characteristics of the films. The results from the surface and depth compositional analyses of the films showed quite good agreement with the energy dispersive X-ray spectroscopy (EDS) analysis.

  13. Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry

    PubMed Central

    Zhou, Wen; Håkansson, Kristina

    2012-01-01

    Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins. PMID:22389641

  14. Better U-Pb Zircon Standards for SIMS and LA-ICPMS? Preliminary Results of Detailed Characterization and Pre-treatment using CA-TIMS

    NASA Astrophysics Data System (ADS)

    Mattinson, J. M.; Hourigan, J.; Wooden, J. L.

    2006-12-01

    U-Pb zircon dating using SIMS and LA-ICPMS requires calibrations against natural zircons of known age. Ideally, such zircons should be perfectly concordant -- free from Pb-loss, inheritance, or any other complications, and also accurately dated. In practice this can be problematic. Complexities can be difficult to detect by SIMS and LA-ICPMS analysis if they are at or below the level of precision of an individual analysis. In addition, conventional TIMS dating, used to date the standards, can be limited by residual minor Pb loss that has not been removed by conventional "pretreatments" such as air abrasion. CA-TIMS (Mattinson, 2005, Chem Geol 220, 47-66) utilizes high-T annealing of natural radiation damage, followed by partial dissolution in HF, and has proven highly successful at complete removal of zircon domains that have experienced Pb loss, both from the outer rims and also from the deep interiors of zircon grains. Thus, it is useful for detailed characterization of existing and potential zircon standards. Here, we also investigate the potential of CA-TIMS for pre-treating zircon standards prior to SIMS and LA-ICPMS analysis. Multi-step CA-TIMS analyses of Temora-2, R-33, and a possible new standard from the Klamath Mountains reveal minor Pb loss in the first few partial dissolution steps, then yield excellent 206Pb*/238 plateau ages, and concordant 207Pb*/206Pb* ages for the remaining steps. Additional aliquots of these zircons were then "pretreated" by CA-TIMS, with sufficient partial dissolution to remove all vestiges of Pb loss, based on the earlier experiments. A sample of AS-57 was pre-treated "blind" because it was received just prior to a scheduled SHRIMP session. All samples were then prepared in a single mount for SHRIMP analysis. Our preliminary results from a round-robin Stanford SHRIMP-RG session using Temora-2, R-33, AS-57, and the Klamath sample are very promising. The Temora-2 and Klamath zircons in particular yielded excellent reproducibility

  15. Structural and functional characterization of the monomeric U-box domain from E4B†

    PubMed Central

    Nordquist, Kyle A.; Dimitrova, Yoana N.; Brzovic, Peter S.; Ridenour, Whitney B.; Munro, Kim A.; Soss, Sarah E.; Caprioli, Richard M.; Klevit, Rachel E.; Chazin, Walter J.

    2009-01-01

    Substantial evidence has accumulated indicating a significant role for oligomerization in the function of E3 ubiquitin ligases. Among the many characterized E3 ligases, the yeast U-box protein Ufd2 and its mammalian homolog E4B appear to be unique in functioning as monomers. An E4B U-box domain construct (E4BU) has been sub-cloned, over-expressed in E. Coli and purified, which enabled determination of a high resolution NMR solution structure and detailed biophysical analysis. E4BU is a stable monomeric protein that folds into the same structure observed for other structurally characterized U-box domains, all of which are homodimers. Multiple sequence alignment combined with comparative structural analysis reveals substitutions in the sequence that inhibit dimerization. The interaction between E4BU and the E2 conjugating enzyme UbcH5c has been mapped using NMR and this data has been used to generate a structural model for the complex. The E2 binding site is found to be similar to that observed for dimeric U-box and RING domain E3 ligases. Despite the inability to dimerize, E4BU was found to be active in a standard autoubiquitination assay. The structure of E4BU and its ability to function as a monomer are discussed in light of the ubiquitous observation of U-box and RING domain oligomerization. PMID:20017557

  16. Microfluidic-based fabrication, characterization and magnetic functionalization of microparticles with novel internal anisotropic structure

    NASA Astrophysics Data System (ADS)

    Qiu, Yang; Wang, Fei; Liu, Ying-Mei; Wang, Wei; Chu, Liang-Yin; Wang, Hua-Lin

    2015-08-01

    Easy fabrication and independent control of the internal and external morphologies of core-shell microparticles still remain challenging. Core-shell microparticle comprised of a previously unknown internal anisotropic structure and a spherical shell was fabricated by microfluidic-based emulsificaiton and photopolymerization. The interfacial and spatial 3D morphology of the anisotropic structure were observed by SEM and micro-CT respectively. Meanwhile, a series of layer-by-layer scans of the anisotropic structure were obtained via the micro-CT, which enhanced the detail characterization and analysis of micro materials. The formation mechanism of the internal anisotropic structure may be attributed to solution-directed diffusion caused by the semipermeable membrane structure and chemical potential difference between inside and outside of the semipermeable membrane-like polymerized shell. The morphology evolution of the anisotropic structure was influenced and controlled by adjusting reaction parameters including polymerization degree, polymerization speed, and solute concentration difference. The potential applications of these microparticles in microrheological characterization and image enhancement were also proposed by embedding magnetic nanoparticles in the inner core.

  17. Microfluidic-based fabrication, characterization and magnetic functionalization of microparticles with novel internal anisotropic structure

    PubMed Central

    Qiu, Yang; Wang, Fei; Liu, Ying-Mei; Wang, Wei; Chu, Liang-Yin; Wang, Hua-Lin

    2015-01-01

    Easy fabrication and independent control of the internal and external morphologies of core-shell microparticles still remain challenging. Core-shell microparticle comprised of a previously unknown internal anisotropic structure and a spherical shell was fabricated by microfluidic-based emulsificaiton and photopolymerization. The interfacial and spatial 3D morphology of the anisotropic structure were observed by SEM and micro-CT respectively. Meanwhile, a series of layer-by-layer scans of the anisotropic structure were obtained via the micro-CT, which enhanced the detail characterization and analysis of micro materials. The formation mechanism of the internal anisotropic structure may be attributed to solution-directed diffusion caused by the semipermeable membrane structure and chemical potential difference between inside and outside of the semipermeable membrane-like polymerized shell. The morphology evolution of the anisotropic structure was influenced and controlled by adjusting reaction parameters including polymerization degree, polymerization speed, and solute concentration difference. The potential applications of these microparticles in microrheological characterization and image enhancement were also proposed by embedding magnetic nanoparticles in the inner core. PMID:26268148

  18. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    The geometrical, structural and geomechanical characterization of large-scale folded structures in sedimentary rocks is an important issue for different geological and geo-hazard applications (e.g. hydrocarbon and geothermal reservoir exploitation, natural rock slope stability, mining, and tunnelling). Fold geometry controls topography and the spatial distribution of rock types with different strength and permeability. Fold-related fracture systems condition the fracture intensity, degree of freedom, and overall strength of rock masses. Nevertheless, scale issues and limited accessibility or partial exposure of structures often hamper a complete characterization of these complex structures. During the last years, advances in remote survey techniques as terrestrial Lidar (TLS) allowed significant improvements in the geometrical and geological characterization of large or inaccessible outcrops. However, sound methods relating structures to rock mass geomechanical properties are yet to be developed. Here we present results obtained by integrating remote survey and field assessment techniques to characterize a folded sedimentary succession exposed in unreachable vertical rock walls. The study area is located in the frontal part of the Southern Alps near Bergamo, Italy. We analysed large-scale detachment folds developed in the Upper Triassic sedimentary cover in the Zu Limestone. Folds are parallel and disharmonic, with regular wavelengths and amplitudes of about 200-250 m. We used a Riegl VZ-1000 long-range laser scanner to obtain points clouds with nominal spacings between 5 cm and 20 cm from 9 scan positions characterized by range between 350 m and 1300 m. We fixed shadowing and occlusion effects related to fold structure exposure by filling point clouds with data collected by terrestrial digital photogrammetry (TDP). In addition, we carried out field surveys of fold-related brittle structures and their geomechanical attributes at key locations. We classified cloud

  19. Characterization of Slosh Damping for Ortho-Grid and Iso-Grid Internal Tank Structures

    NASA Technical Reports Server (NTRS)

    Westra, Douglas G.; Sansone, Marco D.; Eberhart, Chad J.; West, Jeffrey S.

    2016-01-01

    Grid stiffened tank structures such as Ortho-Grid and Iso-Grid are widely used in cryogenic tanks for providing stiffening to the tank while reducing mass, compared to tank walls of constant cross-section. If the structure is internal to the tank, it will positively affect the fluid dynamic behavior of the liquid propellant, in regard to fluid slosh damping. As NASA and commercial companies endeavor to explore the solar system, vehicles will by necessity become more mass efficient, and design margin will be reduced where possible. Therefore, if the damping characteristics of the Ortho-Grid and Iso-Grid structure is understood, their positive damping effect can be taken into account in the systems design process. Historically, damping by internal structures has been characterized by rules of thumb and for Ortho-Grid, empirical design tools intended for slosh baffles of much larger cross-section have been used. There is little or no information available to characterize the slosh behavior of Iso-Grid internal structure. Therefore, to take advantage of these structures for their positive damping effects, there is much need for obtaining additional data and tools to characterize them. Recently, the NASA Marshall Space Flight Center conducted both sub-scale testing and computational fluid dynamics (CFD) simulations of slosh damping for Ortho-Grid and Iso-Grid tanks for cylindrical tanks containing water. Enhanced grid meshing techniques were applied to the geometrically detailed and complex Ortho-Grid and Iso-Grid structures. The Loci-STREAM CFD program with the Volume of Fluid Method module for tracking and locating the water-air fluid interface was used to conduct the simulations. The CFD simulations were validated with the test data and new empirical models for predicting damping and frequency of Ortho-Grid and Iso-Grid structures were generated.

  20. RF and structural characterization of new SRF films

    SciTech Connect

    A.-M. Valente-Feliciano,H. L. Phillips,C. E. Reece,X. Zhao,D. Gu,R. Lukaszew,B. Xiao,K. Seo

    2009-09-01

    In the past years, energetic vacuum deposition methods have been developed in different laboratories to improve Nb/Cu technology for superconducting cavities. Jefferson Lab is pursuing energetic condensation deposition via Electron Cyclotron Resonance. As part of this study, the influence of the deposition energy on the material and RF properties of the Nb thin film is investigated. The film surface and structure analyses are conducted with various techniques like X-ray diffraction, Transmission Electron Microscopy, Auger Electron Spectroscopy and RHEED. The microwave properties of the films are characterized on 50 mm disk samples with a 7.5 GHz surface impedance characterization system. This paper presents surface impedance measurements in correlation with surface and material characterization for Nb films produced on copper substrates with different bias voltages and also highlights emerging opportunities for developing multilayer SRF films with a new deposition system.

  1. Characterization of coherent structures in the cardiovascular system.

    PubMed

    Shadden, Shawn C; Taylor, Charles A

    2008-07-01

    Recent advances in blood flow modeling have provided highly resolved, four-dimensional data of fluid mechanics in large vessels. The motivation for such modeling is often to better understand how flow conditions relate to health and disease, or to evaluate interventions that affect, or are affected by, blood flow mechanics. Vessel geometry and the pulsatile pumping of blood leads to complex flow, which is often difficult to characterize. This article discusses a computational method to better characterize blood flow kinematics. In particular, we compute Lagrangian coherent structures (LCS) to study flow in large vessels. We demonstrate that LCS can be used to characterize flow stagnation, flow separation, partitioning of fluid to downstream vasculature, and mechanisms governing stirring and mixing in vascular models. This perspective allows valuable understanding of flow features in large vessels beyond methods traditionally considered.

  2. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    NASA Astrophysics Data System (ADS)

    Kozlov, M. E.; Murthy, N. S.; Udod, I.; Khayrullin, I. I.; Baughman, R. H.; Zakhidov, A. A.

    2007-03-01

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO2 sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO2 lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time.

  3. Structural and functional characterization of synapse-associated protein-97

    NASA Astrophysics Data System (ADS)

    Wang, Lei

    Synapse-associated protein-97 (SAP97) as a scaffold protein plays an important role in regulating neural signal transmission in the central nervous system by coupling with activated membrane receptors, ion channels, and downstream signaling proteins. SAP97 consists of six functional domains: L27, PDZ1, PDZ2, PDZ3, SH3, and GK. Each of these domains mediates the interactions of SAP97 with other proteins. Understanding the molecular mechanism of these interactions in neural signal transmission is a goal of this study. Here high-resolution nuclear magnetic resonance spectroscopy and fluorescence anisotropy are employed towards the goal of the structural and functional characterization of SAP97; specifically, we (a) characterize the binding of the PDZ domains of SAP97 with the C-terminus of NR2B, and determine the structure of the PDZ1-NR2B; (b) characterize the binding of the PDZ domains with the C-terminus of stargazin and multiple mutants, and identify the perturbed amino acids in PDZ2 upon the binding of stargazin; (c) characterize the binding specificity carried by the beta2/beta3 loop of the PDZ3 domain. These results provide insight into the molecular mechanism for the binding specificities of the PDZ domains of SAP97, thereby furthering the development of drugs that target these domains to treat neurological diseases.

  4. Characterization of seismic hazard and structural response by energy flux

    USGS Publications Warehouse

    Afak, E.

    2000-01-01

    Seismic safety of structures depends on the structure's ability to absorb the seismic energy that is transmitted from ground to structure. One parameter that can be used to characterize seismic energy is the energy flux. Energy flux is defined as the amount of energy transmitted per unit time through a cross-section of a medium, and is equal to kinetic energy multiplied by the propagation velocity of seismic waves. The peak or the integral of energy flux can be used to characterize ground motions. By definition, energy flux automatically accounts for site amplification. Energy flux in a structure can be studied by formulating the problem as a wave propagation problem. For buildings founded on layered soil media and subjected to vertically incident plane shear waves, energy flux equations are derived by modeling the buildings as an extension of the layered soil medium, and considering each story as another layer. The propagation of energy flux in the layers is described in terms of the upgoing and downgoing energy flux in each layer, and the energy reflection and transmission coefficients at each interface. The formulation results in a pair of simple finite-difference equations for each layer, which can be solved recursively starting from the bedrock. The upgoing and downgoing energy flux in the layers allows calculation of the energy demand and energy dissipation in each layer. The methodology is applicable to linear, as well as nonlinear structures. ?? 2000 Published by Elsevier Science Ltd.

  5. Optical fiber sensors for materials and structures characterization

    NASA Technical Reports Server (NTRS)

    Lindner, D. K.; Claus, R. O.

    1991-01-01

    The final technical report on Optical Fiber Sensors for Materials and Structures Characterization, covering the period August 1990 through August 1991 is presented. Research programs in the following technical areas are described; sapphire optical fiber sensors; vibration analysis using two-mode elliptical core fibers and sensors; extrinsic Fabry-Perot interferometer development; and coatings for fluorescent-based sensor. Research progress in each of these areas was substantial, as evidenced by the technical publications which are included as appendices.

  6. Details of meiosis

    SciTech Connect

    1993-12-31

    Chapter 18, discusses the details of meiosis, beginning with the structure and number of chiasmata, i.e., the cytological term for two homologous chromosomes forming a bivalent which begin to repel each other until they are held together only at the point of crossing-over. The synaptonemal complex which consists of two lateral elements which contain protein and RNA is also discussed. The chapter concludes with a description of meiosis in polyploids, human meiosis, and the behavior of X and Y chromosomes. 28 refs., 8 figs.

  7. Statistical characterizations of rainfall structure over two tropical stations in southern India for microwave communication

    NASA Astrophysics Data System (ADS)

    Ojo, J. S.; Ajewole, M. O.; Sarkar, S. K.

    2010-08-01

    Statistical characterizations of rainfall structure over two tropical stations in southern India are reported in this paper based on the 2-year rainfall data. The statistical characterizations has been based on cumulative distribution function, exceedance of threshold values, dependence of the intensity of rainfall on the event duration, seasonal variability, and worst months concept as well as diurnal variability. These results are needed to give the detailed insights to the system designers for the development of communication gadgets needed for better service, serve as a vital tool to estimate signal outages in a year over the region and for proper planning of radio communication in the region. Finally, the study shows that the recent International Telecommunications Union Recommendations (ITU-R) value underestimated rain rate for 0.01% exceedance for the two locations.

  8. Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure

    PubMed Central

    Araya-Secchi, Raul; Perez-Acle, Tomas; Kang, Seung-gu; Huynh, Tien; Bernardin, Alejandro; Escalona, Yerko; Garate, Jose-Antonio; Martínez, Agustin D.; García, Isaac E.; Sáez, Juan C.; Zhou, Ruhong

    2014-01-01

    Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket—termed the IC pocket—located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability. PMID:25099799

  9. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    USGS Publications Warehouse

    Bargar, J.R.; Fuller, C.C.; Marcus, M.A.; Brearley, A.J.; Perez De la Rosa, M.; Webb, S.M.; Caldwell, W.A.

    2009-01-01

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick ?? 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-?? basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments. ?? 2008 Elsevier Ltd.

  10. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    SciTech Connect

    Bargar, John; Fuller, Christopher; Marcus, Matthew A.; Brearley, Adrian J.; Perez De la Rosa, M.; Webb, Samuel M.; Caldwell, Wendel A.

    2008-03-19

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick x 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-A basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mnoxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.

  11. (abstract) Characterization of Structural Response for Systems with Loose Joints

    NASA Technical Reports Server (NTRS)

    Bruno, Robin J.

    1995-01-01

    This paper describes a technique to locate and characterize loose joints in a large truss structure to generate an accurate structural model. The joint looseness is modeled as a gap in the member that opens and closes depending on the loading. Arbitrarily placed actuators are used to prestress the structure to first linearize the response. Next the actuator displacements are systematically reduced while monitoring the displacement response. The gap locations are determined by comparing the measured displacements with sets of calculated displacements and the sizes are estimated by monitoring the gap member length changes using the appropriate linear force-displacement relationship for the load level. The effect of measurement error in the truss displacements and the actuator length changes are investigated.

  12. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael Nishi, Yoshio; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero

    2015-11-02

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. We measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  13. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero; Nishi, Yoshio

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  14. Detailed transient heme structures of Mb-CO in solution after CO dissociation: an X-ray transient absorption spectroscopic study.

    PubMed

    Stickrath, Andrew B; Mara, Michael W; Lockard, Jenny V; Harpham, Michael R; Huang, Jier; Zhang, Xiaoyi; Attenkofer, Klaus; Chen, Lin X

    2013-04-25

    Although understanding the structural dynamics associated with ligand photodissociation is necessary in order to correlate structure and function in biological systems, few techniques are capable of measuring the ultrafast dynamics of these systems in solution-phase at room temperature. We present here a detailed X-ray transient absorption (XTA) study of the photodissociation of CO-bound myoglobin (Fe(II)CO-Mb) in room-temperature aqueous buffer solution with a time resolution of 80 ps, along with a general procedure for handling biological samples under the harsh experimental conditions that transient X-ray experiments entail. The XTA spectra of (Fe(II)CO-Mb) exhibit significant XANES and XAFS alterations following 527 nm excitation, which remain unchanged for >47 μs. These spectral changes indicate loss of the CO ligand, resulting in a five-coordinate, domed heme, and significant energetic reorganization of the 3d orbitals of the Fe center. With the current experimental setup, each X-ray pulse in the pulse train, separated by ~153 ns, can be separately discriminated, yielding snapshots of the myoglobin evolution over time. These methods can be easily applied to other biological systems, allowing for simultaneous structural and electronic measurements of any biological system with both ultrafast and slow time resolutions, effectively mapping out all of the samples' relevant physiological processes.

  15. Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants.

    PubMed

    Ruszkowski, Milosz; Dauter, Zbigniew

    2016-05-06

    The penultimate enzyme in the histidine biosynthetic pathway catalyzes dephosphorylation of l-histidinol 1-phosphate (HOLP) into l-histidinol. The recently discovered in Arabidopsis thaliana plant-type histidinol phosphate phosphatase (HPP) shares no homology with the two other HPP superfamilies known previously in prokaryotes and resembles myo-inositol monophosphatases (IMPases). In this work, identification of an HPP enzyme from a model legume, Medicago truncatula (MtHPP) was based on the highest sequence identity to A. thaliana enzyme. Biochemical assays confirmed that MtHPP was able to cleave inorganic phosphate from HOLP but not from d-myo-inositol-1-phosphate, the main substrate of IMPases. Dimers of MtHPP, determined by size exclusion chromatography, in the presence of CO2 or formaldehyde form mutual, methylene-bridged cross-links between Lys(158) and Cys(245) residues. Four high resolution crystal structures, namely complexes with HOLP (substrate), l-histidinol (product), and PO4 (3-) (by-product) as well as the structure showing the cross-linking between two MtHPP molecules, provide detailed structural information on the enzyme. Based on the crystal structures, the enzymatic reaction mechanism of IMPases is accustomed to fit the data for MtHPP. The enzymatic reaction, which requires Mg(2+) cations, is catalyzed mainly by amino acid residues from the N-terminal domain. The C-terminal domain, sharing little identity with IMPases, is responsible for the substrate specificity (i.e. allows the enzyme to distinguish between HOLP and d-myo-inositol-1-phosphate). Structural features, mainly the presence of a conserved Asp(246), allow MtHPP to bind HOLP specifically.

  16. Characterization of graphene-nanoplatelets structure via thermogravimetry.

    PubMed

    Shtein, Michael; Pri-Bar, Ilan; Varenik, Maxim; Regev, Oren

    2015-04-21

    The rapid increase in graphene-based applications has been accompanied by novel top-down manufacturing methods for graphene and its derivatives (e.g., graphene nanoplatelets (GnPs)). The characterization of the bulk properties of these materials by imaging and surface techniques (e.g., electron microscopy and Raman spectroscopy) is only possible through laborious and time-consuming statistical analysis, which precludes simple and efficient quality control during GnP production. We report that thermogravimetry (TG) may be utilized, beyond its conventional applications (e.g., quantification of impurities or surfactants, or labile functional groups) to characterize bulk GnP properties. We characterize the structural parameters of GnP (i.e., defect density, mean lateral dimension, and polydispersity) by imaging and surface techniques, on one hand, and by a systematic TG, on the other. The combined data demonstrate that the combustion temperature of commercially available and laboratory-prepared GnPs is correlated with their mean lateral dimension and defect density, while the combustion temperature range is proportional to their polydispersity index. Mapping all these parameters allows one to evaluate the GnPs' structure following a simple thermogravimetric experiment (without necessitating further statistical analysis). Finally, TG is also used to detect and quantify different GnP constituents in powder and to conduct rapid quality-control tests during GnP production.

  17. High-density properties of integral-equation theories of fluids: Universal analytic structure and details for the one-component plasma

    NASA Astrophysics Data System (ADS)

    Rosenfeld, Yaakov

    1986-03-01

    We study the analytic properties of the hypernetted-chain (HNC) and soft-mean-spherical (SMSA) theories in the asymptotic high-density limit (AHDL). The scaling properties of the inverse power potentials lead to the introduction of the SMSA-Ewald functions, which correspond to the ``overlap-volume'' functions for hard spheres. The HNC and SMSA theories for soft interactions, as well as the Percus-Yevick theory for hard spheres, feature the same AHDL analytic structure of the pair correlation functions, which is dictated by the hard-sphere Ewald functions. The general discussion is supplemented by detailed results for the one-component plasma. Implications to the analysis of the density-functional theory, of dense matter, near its exact Thomas-Fermi limit are pointed out.

  18. Revealing the Detailed Structure of the Galactic Core-Collapse Supernova Remnant G292.0+1.8 with X-Ray Mapping

    NASA Astrophysics Data System (ADS)

    Bhalerao, Jayant; Park, Sangwook; Schenck, Andrew

    2017-01-01

    We present our results on the adaptive-mesh mapping of the chemical composition and thermodynamic parameters of the Galactic core-collapse supernova remnant G292.0+1.8 using our deep Chandra observation. Our maps cover the entire supernova remnant and show the detailed spatial distributions of the metal-rich ejecta, circumstellar medium, and the X-ray pulsar wind nebula-dominated regions. Our results suggest radial and azimuthal variations in the ejecta composition and the thermodynamic parameters, underscoring the rich and complex nature of this text book type supernova remnant. Combining our results from this study and our previous work on the ejecta radial velocity distribution (derived from our Chandra HETG data), we discuss the three dimensional structure of the remnant. Some implications on the nature of the progenitor star and explosion scenarios are discussed.

  19. Structural characterizations of the chloroplast translocon protein Tic110

    PubMed Central

    Tsai, Jia-Yin; Chu, Chiung-Chih; Yeh, Yi-Hung; Chen, Lih-Jen; Li, Hsou-min; Hsiao, Chwan-Deng

    2013-01-01

    Tic110 is a major component of the chloroplast protein import translocon. Two functions with mutually exclusive structures have been proposed for Tic110: a protein-conducting channel with six transmembrane domains and a scaffold with two N-terminal transmembrane domains followed by a large soluble domain for binding transit peptides and other stromal translocon components. To investigate the structure of Tic110, Tic110 from Cyanidioschyzon merolae (CmTic110) was characterized. We constructed three fragments, CmTic110A, CmTic110B and CmTic110C, with increasing N-terminal truncations, to perform small-angle X-ray scattering (SAXS) and X-ray crystallography analyses and Dali structural comparison. Here we report the molecular envelope of CmTic110B and CmTic110C determined by SAXS, and the crystal structure of CmTic110C at 4.2 Å. Our data indicate that the C-terminal half of CmTic110 possesses a rod-shaped helix-repeat structure that is too flattened and elongated to be a channel. The structure is most similar to the HEAT-repeat motif that functions as scaffolds for protein–protein interactions. PMID:23711301

  20. Characterization of photonic amorphous structures with different characteristic lengths

    NASA Astrophysics Data System (ADS)

    Wen, Cheng-Chi; Hung, Yu-Chueh

    2016-04-01

    Photonic amorphous structure (PAS) has attracted increasing research attention due to their interesting characteristics, such as noniridescent structural colors and isotropic photonic band gap. In this work, we present PAS with different characteristic lengths and analyze their structural and topological properties. First, a Fourier spectral method was used to solve Cahn-Hilliard equation and generate a spinodal binary phase structure. By changing the time of the evolution of phase field, mobility, and standard deviation, the characteristic length of amorphous structures can be adjusted. We present the numerical analysis based on finite-difference time-domain (FDTD) method to characterize the density of state (DOS) of PAS based on different time of the evolution of phase field. The corresponding spatial Fourier spectrum of PAS is calculated to examine the characteristic length, and the photonic band gap properties will be discussed in association with the characteristic length. These results are crucial for design of new optical materials display devices base on dielectric amorphous photonic structures.

  1. Comparing the Performance of Three Land Models in Global C Cycle Simulations: A Detailed Structural Analysis: Structural Analysis of Land Models

    SciTech Connect

    Rafique, Rashid; Xia, Jianyang; Hararuk, Oleksandra; Leng, Guoyong; Asrar, Ghassem; Luo, Yiqi

    2016-04-01

    Land models are valuable tools to understand the dynamics of global carbon (C) cycle. Various models have been developed and used for predictions of future C dynamics but uncertainties still exist. Diagnosing the models’ behaviors in terms of structures can help to narrow down the uncertainties in prediction of C dynamics. In this study three widely used land surface models, namely CSIRO’s Atmosphere Biosphere Land Exchange (CABLE) with 9 C pools, Community Land Model (version 3.5) combined with Carnegie-Ames-Stanford Approach (CLM-CASA) with 12 C pools and Community Land Model (version 4) (CLM4) with 26 C pools were driven by the observed meteorological forcing. The simulated C storage and residence time were used for analysis. The C storage and residence time were computed globally for all individual soil and plant pools, as well as net primary productivity (NPP) and its allocation to different plant components’ based on these models. Remotely sensed NPP and statistically derived HWSD, and GLC2000 datasets were used as a reference to evaluate the performance of these models. Results showed that CABLE exhibited better agreement with referenced C storage and residence time for plant and soil pools, as compared with CLM-CASA and CLM4. CABLE had longer bulk residence time for soil C pools and stored more C in roots, whereas, CLM-CASA and CLM4 stored more C in woody pools due to differential NPP allocation. Overall, these results indicate that the differences in C storage and residence times in three models are largely due to the differences in their fundamental structures (number of C pools), NPP allocation and C transfer rates. Our results have implications in model development and provide a general framework to explain the bias/uncertainties in simulation of C storage and residence times from the perspectives of model structures.

  2. Synthesis and structural characterization of hydrolysis products within the uranyl iminodiacetate and malate systems.

    PubMed

    Unruh, Daniel K; Gojdas, Kyle; Flores, Erin; Libo, Anna; Forbes, Tori Z

    2013-09-03

    The interplay of hydrolysis and chelation by organic ligands results in the formation of novel uranium species in aqueous solutions. Many of these molecular complexes have been identified by spectroscopic and potentiometric techniques, but a detailed structural understanding of these species is lacking. Identification of possible uranyl hydrolysis products in the presence of organic functional groups has been achieved by the crystallization of molecular species into a solid-state compound, followed by structural and chemical characterization of the material. The structures of three novel molecular complexes containing either iminodiacetate (ida) (Na3[(UO2)3(OH)3(ida)3]·8H2O (1)) or malate (mal) (K(pip)2[(UO2)3O(mal)3]·6H2O (2a) (pip = C4N2H12), (2b) (pip)3[(UO2)3O(mal)3]·H2O, and (pip)6[(UO2)11(O)4(OH)4(mal)6(CO3)2]·23H2O (3)) ligands have been determined by single-crystal X-ray diffraction and have been chemically characterized by IR, Raman, and NMR spectroscopies. A major structural component in compounds 1 and 2 is a trimeric 3:3 uranyl ida or mal species, but different bridging groups between the metal centers create variations in the structural topologies of the molecular units. Compound 3 contains a large polynuclear cluster with 11 U atoms, which is composed of trimeric and pentameric building units chelated by mal ligands and linked through hydroxyl groups and carbonate anions. The characterized compounds represent novel structural topologies for U(6+) hydrolysis products that may be important molecular species in near-neutral aqueous systems.

  3. Structural Implications of new Geologic Mapping and a Detailed Gravity Traverse in the Brooks Range Foothills, Chandler Lake Quadrangle, Northern Alaska

    NASA Astrophysics Data System (ADS)

    Peapples, P. R.; Saltus, R. W.; Swenson, R.; Brown, P. J.

    2005-12-01

    A fold and thrust belt in northern Alaska occupies the structural transition from the imbricate thrust sheets (or allochthons) of the Brooks Range to the North Slope coastal plain. Understanding this complexly deformed zone is critical to hydrocarbon assessment in the state-owned lands south of Prudhoe Bay. New geologic mapping and geophysical studies are focused on this important region. Detailed (1:63,360 scale) geologic mapping along the drainages of Tiglukpuk Creek and the Siksikpuk River documents exposures of deep structural levels and provides important constraints for a structural model of this region. A south-to-north structural transect encompasses the transition from the highly deformed thrust sheets of the Endicott Mountains Allochthon (EMA) at the mountain front to the inferred triangle zone at the Tuktu Escarpment 45 miles to the north. Mississippian Carbonates to Triassic siliciclastics make up the EMA north of the mountain front where there is an abrupt transition in structural style from north-vergent asymmetric overturned folding to gentle warping above shallowly dipping fault ramps. Tiglukpuk Anticline represents a fenster where the EMA is overlain in thrust contact by a melange of more distal Ipnavik River Allochthon (IRA) rocks. Parallel synclinoria contain the Okpikruak siliciclastics of the IRA assemblage and the Brookian syntectonic siliciclastics of the Fortress Mountain formation, carried atop the EMA thrust sheets during the latest phase of deformation. This complex structural style abruptly ends at the Tuktu Escarpment which likely represents a backthrust/triangle zone that places shallow north dipping coarse clastics of the Nanushuk Formation over the less competent and highly deformed Torok shale. The structural complexity and associated steeply dipping strata in the foothills belt were not well imaged by existing conventional seismic data in this region. To provide additional subsurface control, we collected ground station gravity

  4. Detailed structure of the Philippine Sea plate subducting along the Nankai Trough, western Japan, inferred from high-frequency seismic wave analysis

    NASA Astrophysics Data System (ADS)

    Furumura, T.; Padhy, S.; Maeda, T.

    2012-12-01

    A detailed structure of the subducting Philippine Sea plate (PHP) along the Nankai trough in western Japan was studied by analyzing waveforms recorded at dense Hi-net stations in Japan. It is well recognized that the waveforms from intraplate earthquakes dominate in high-frequency (f >1 Hz) signals due to the waveguide effect of the subducting slab (Furumura and Kennett, 2005; 2008). This results in distorted pattern of intensity and peak ground acceleration (PGA) above the hypocenter with a substantial elongation of isoseismic contours correlated with the configuration of the isodepth contours of the subducting PHP beneath western Japan. A detailed analysis of the dense Hi-net waveform data from the intermediate-depth PHP event shows that the high-frequency S-wave signals suddenly disappear as the waves propagate the zone away from the Kii Channel to the boundary of Hyogo and Okayama prefectures and large S-to-P conversion occurs before the arrival of S-wave. Such anomalies do not occur for shallow and deep earthquakes occurring outside the PHP. These observations support the recent debate on the complexities of the configuration of the PHP subducting beneath western Japan such as that shown by Shiomi et al. (2008) based on receiver function images and the PHP-split model beneath the Kii channel shown by Ide et al.(2010) based on the analysis of comprehensive geophysical data. In order to explain the observations associated with sudden lateral change in the PHP structure, we conducted finite difference method (FDM) simulations of seismic wave propagation taking the detailed PHP model into account. It is confirmed that high-frequency guided wave energy decouple from waveguide where the shape of the PHP is suddenly deformed, which results in dramatic attenuation of high-frequency signals associating with large S-to-P conversions developed at sharp plate boundary. The present results also support the recently proposed complicated PHP-split model, however, further

  5. Biophysical characterization of recombinant proteins: A key to higher structural genomics success

    PubMed Central

    Vedadi, Masoud; Arrowsmith, Cheryl H.; Allali-Hassani, Abdellah; Senisterra, Guillermo; Wasney, Gregory A.

    2010-01-01

    Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have paved the way for structural genomics efforts. Frequently, however, little is known about newly expressed proteins calling for large-scale protein characterization to better understand their biochemical roles and to enable structure–function relationship studies. In the Structural Genomics Consortium (SGC), we have established a platform to characterize large numbers of purified proteins. This includes screening for ligands, enzyme assays, peptide arrays and peptide displacement in a 384-well format. In this review, we describe this platform in more detail and report on how our approach significantly increases the success rate for structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, this platform can also be used toward the development of chemical probes through screening families of proteins against a variety of chemical series and focused chemical libraries. PMID:20466062

  6. Characterization of cuttlebone for a biomimetic design of cellular structures

    NASA Astrophysics Data System (ADS)

    Cadman, Joseph; Zhou, Shiwei; Chen, Yuhang; Li, Wei; Appleyard, Richard; Li, Qing

    2010-03-01

    Cuttlebone is a natural material possessing the multifunctional properties of high porosity, high flexural stiffness and compressive strength, making it a fine example of design optimization of cellular structures created by nature. Examination of cuttlebone using scanning electron microscopy (SEM) reveals an approximately periodic microstructure, appropriate for computational characterization using direct homogenization techniques. In this paper, volume fractions and stiffness tensors were determined based on two different unit cell models that were extracted from two different cuttlefish samples. These characterized results were then used as the target values in an inverse homogenization procedure aiming to re-generate microstructures with the same properties as cuttlebone. Unit cells with similar topologies to the original cuttlebone unit cells were achieved, attaining the same volume fraction (i.e. bulk density) and the same (or very close) stiffness tensor. In addition, a range of alternate unit cell topologies were achieved also attaining the target properties, revealing the non-unique nature of this inverse homogenization problem.

  7. Characterization of localized transverse structures in wide-aperture lasers

    NASA Astrophysics Data System (ADS)

    Rosanov, N. N.; Fedorov, A. V.; Fedorov, S. V.; Khodova, G. V.

    The problem of characterization of spatio-temporal patterns is discussed for the case of wide-aperture lasers with nonlinear losses where variety of such patterns is especially rich. Laser autosolitons (LASs)-localized transverse structures representing “islands of lasing” on a background of the nonlasing mode on the laser aperture-are studied. Existence of stable single LASs which are motionless or moving in the transverse direction with constant linear velocity is shown. Described are also LASs with regular wavefronts, those with screw dislocations (defects) of wavefronts with different topological indices, and those with axially symmetric and asymmetric intensity distributions rotating with constant angular velocity around the LAS center. An approach is given for qualitative and quantitative characterization of a single LAS by its linear and angular velocities and frequency shift, based on a combination of analytical methods and computer simulations. Results of investigations of weak and strong interactions among the LASs are presented.

  8. Structural and compositional characterization of the adhesive produced by reef building oysters.

    PubMed

    Alberts, Erik M; Taylor, Stephen D; Edwards, Stephanie L; Sherman, Debra M; Huang, Chia-Ping; Kenny, Paul; Wilker, Jonathan J

    2015-04-29

    Oysters have an impressive ability to overcome difficulties of life within the stressful intertidal zone. These shellfish produce an adhesive for attaching to each other and building protective reef communities. With their reefs often exceeding kilometers in length, oysters play a major role in balancing the health of coastal marine ecosystems. Few details are available to describe oyster adhesive composition or structure. Here several characterization methods were applied to describe the nature of this material. Microscopy studies indicated that the glue is comprised of organic fiber-like and sheet-like structures surrounded by an inorganic matrix. Phospholipids, cross-linking chemistry, and conjugated organics were found to differentiate this adhesive from the shell. Symbiosis in material synthesis could also be present, with oysters incorporating bacterial polysaccharides into their adhesive. Oyster glue shows that an organic-inorganic composite material can provide adhesion, a property especially important when constructing a marine ecosystem.

  9. EDITORIAL: (Nano)characterization of semiconductor materials and structures (Nano)characterization of semiconductor materials and structures

    NASA Astrophysics Data System (ADS)

    Bonanni, Alberta

    2011-06-01

    The latest impressive advancements in the epitaxial fabrication of semiconductors and in the refinement of characterization techniques have the potential to allow insight into the deep relation between materials' structural properties and their physical and chemical functionalities. Furthermore, while the comprehensive (nano)characterization of semiconductor materials and structures is becoming more and more necessary, a compendium of the currently available techniques is lacking. We are positive that an overview of the hurdles related to the specific methods, often leading to deceptive interpretations, will be most informative for the broad community working on semiconductors, and will help in shining some light onto a plethora of controversial reports found in the literature. From this perspective, with this special issue we address and highlight the challenges and misinterpretations related to complementary local (nanoscale) and more global experimental methods for the characterization of semiconductors. The six topical reviews and the three invited papers by leading experts in the specific fields collected in here are intended to provide the required broad overview on the possibilities of actual (nano)characterization methods, from the microscopy of single quantum structures, over the synchrotron-based absorption and diffraction of nano-objects, to the contentious detection of tiny magnetic signals by quantum interference and resonance techniques. We are grateful to all the authors for their valuable contributions. Moreover, I would like to thank the Editorial Board of the journal for supporting the realization of this special issue and for inviting me to serve as Guest Editor. We greatly appreciate the work of the reviewers, of the editorial staff of Semiconductor Science and Technology and of IOP Publishing. In particular, the efforts of Alice Malhador in coordinating this special issue are acknowledged.

  10. Characterization of the nanoscale structure of milk fat.

    PubMed

    Ramel, Pere Randy R; Peyronel, Fernanda; Marangoni, Alejandro G

    2016-07-15

    The nanoscale structure of milk fat (MF) crystal networks is extensively described for the first time through the characterization of milk fat-crystalline nanoplatelets (MF-CNPs). Removing oil by washing with cold isobutanol and breaking-down crystal aggregates by controlled homogenization allowed for the extraction and visualization of individual MF-CNPs that are mainly composed of high melting triacylglycerols (TAGs). By image analysis, the length and width of MF-CNPs were measured (600 nm × 200 nm-900 nm × 300 nm). Using small-angle X-ray scattering (SAXS), crystalline domain size, (i.e., thickness of MF-CNPs), was determined (27 nm (d001)). Through interpretation of ultra-small-angle X-ray scattering (USAXS) patterns of MF using Unified Fit and Guinier-Porod models, structural properties of MF-CNPs (smooth surfaces) and MF-CNP aggregations were characterized (RLCA aggregation of MF-CNPs to form larger structures that present diffused surfaces). Elucidation of MF-CNPs provides a new dimension of analysis for describing MF crystal networks and opens-up opportunities for modifying MF properties through nanoengineering.

  11. Function Discovery and Structural Characterization of a Methylphosphonate Esterase

    PubMed Central

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V.; Toro, Rafael; Almo, Steven C.; Raushel, Frank M.

    2015-01-01

    Pmi1525, an enzyme of unknown function from Proteus Mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s−1 and 1.2 × 105 M−1 s−1, respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s−1 and 1.4 × 105 M−1 s−1, respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents. PMID:25873441

  12. The electronic structure and second-order nonlinear optical properties of donor-acceptor acetylenes - A detailed investigation of structure-property relationships

    NASA Technical Reports Server (NTRS)

    Stiegman, A. E.; Graham, Eva; Khundkar, Lutfur R.; Perry, Joseph W.; Cheng, L.-T.; Perry, Kelly J.

    1991-01-01

    A series of donor-acceptor acetylene compounds was synthesized in which systematic changes in both the conjugation length and the donor-acceptor strength were made. The effect of these structural changes on the spectroscopic and electronic properties of the molecules and, ultimately, on the measured second-order molecular hyperpolarizabilities (beta) was investigated. It was found that increases in the donor-acceptor strength resulted in increases in the magnitude of beta. For this class of molecules, the increase is dominated by the energy of the intramolecular charge-transfer transition, while factors such as the ground to excited-state dipole moment change and the transition-moment integral are much less important. Increasing the conjugation length from one to two acetylene linkers did not result in an increase in the value of beta; however, beta increased sharply in going from two acetylenes to three. This increase is attributed to the superposition of several nearly isoenergetic excited states.

  13. Rapid Characterization of Vegetation Structure with a Microsoft Kinect Sensor

    PubMed Central

    Azzari, George; Goulden, Michael L.; Rusu, Radu B.

    2013-01-01

    The importance of vegetation structure and biomass in controlling land-atmosphere exchange is widely recognized, but measurements of canopy structure are challenging, time consuming, and often rely on destructive methods. The Microsoft Kinect is an infrared sensor designed for video gaming that outputs synchronized color and depth images and that has the potential to allow rapid characterization of vegetation structure. We compared depth images from a Kinect sensor with manual measurements of plant structure and size for two species growing in a California grassland. The depth images agreed well with the horizontal and vertical measurements of plant size made manually. Similarly, the plant volumes calculated with a three-dimensional convex hulls approach was well related to plant biomass. The Kinect showed some limitations for ecological observation associated with a short measurement range and daytime light contamination. Nonetheless, the Kinect's light weight, fast acquisition time, low power requirement, and cost make it a promising tool for rapid field surveys of canopy structure, especially in small-statured vegetation. PMID:23435053

  14. Characterizing Englacial and Subglacial Temperature Structure Using Airborne Radar Sounding

    NASA Astrophysics Data System (ADS)

    Schroeder, D. M.; Seroussi, H. L.

    2015-12-01

    The temperature structure of ice sheet and glaciers is a fundamental control on ice flow, rheology, and stability. However, it is difficult to observationally constrain temperature structures at the catchment to ice-sheet scale. The englacial attenuation of radar sounding data is strongly dependent on the temperature structure of the ice sheets. Therefore, echo strength profiles from airborne radar sounding observation do contain temperature information. However, direct interpretation of englacial attenuation rates from radar sounding profiles is often difficult or impossible due to the ambiguous contribution the geometric and material properties of the bed to echo strength variations. To overcome this challenge, we presents techniques that treat radar sounding echo strength and ice thickness profiles as continuous signals, taking advantage of along-profile ice thickness and echo strength variations to constrain the spatial pattern of englacial attenuation and basal reflectivity. We then apply these techniques to an airborne radar sounding survey in order to characterize the englacial and subglacial temperature structure of the Thwaites Glacier catchment in West Antarctic. We then interpreted this structure in context of local ice sheet velocity, advection, force balance, and bed conditions using the ISSM ice sheet model.

  15. Rapid characterization of vegetation structure with a Microsoft Kinect sensor.

    PubMed

    Azzari, George; Goulden, Michael L; Rusu, Radu B

    2013-02-11

    The importance of vegetation structure and biomass in controlling land-atmosphere exchange is widely recognized, but measurements of canopy structure are challenging, time consuming, and often rely on destructive methods. The Microsoft Kinect is an infrared sensor designed for video gaming that outputs synchronized color and depth images and that has the potential to allow rapid characterization of vegetation structure. We compared depth images from a Kinect sensor with manual measurements of plant structure and size for two species growing in a California grassland. The depth images agreed well with the horizontal and vertical measurements of plant size made manually. Similarly, the plant volumes calculated with a three-dimensional convex hulls approach was well related to plant biomass. The Kinect showed some limitations for ecological observation associated with a short measurement range and daytime light contamination. Nonetheless, the Kinect's light weight, fast acquisition time, low power requirement, and cost make it a promising tool for rapid field surveys of canopy structure, especially in small-statured vegetation.

  16. Structural characterization of impurified zinc oxide thin films

    SciTech Connect

    Trinca, L. M.; Galca, A. C. Stancu, V. Chirila, C. Pintilie, L.

    2014-11-05

    Europium doped zinc oxide (Eu:ZnO) thin films have been obtained by pulsed laser deposition (PLD). 002 textured thin films were achieved on glass and silicon substrates, while hetero-epilayers and homo-epilayers have been attained on single crystal SrTiO{sub 3} and ZnO, respectively. X-ray Diffraction (XRD) was employed to characterize the Eu:ZnO thin films. Extended XRD studies confirmed the different thin film structural properties as function of chosen substrates.

  17. Isolation and structural characterization of anthocyanin-furfuryl pigments.

    PubMed

    Sousa, André; Mateus, Nuno; Silva, Artur Manuel Soares; Vivas, Nicolas; Nonier, Marie-Françoise; Pianet, Isabelle; de Freitas, Victor

    2010-05-12

    Condensation reactions of malvidin-3-glucoside with two representative oak wood furanic aldehydes (furfural and methylfurfural) were conducted in wine-like model solutions. Methylfurfural led to the formation of malvidin-3-glucoside-methylfurfural (603 m/z), whereas furfural led to the formation of malvidin-3-glucoside-furfural (589 m/z). The latter was structurally characterized by 1D and 2D NMR, allowing an elucidation of the formation mechanism of these anthocyanin-furanic aldehyde adducts in the absence of flavanols.

  18. Use of thermal imaging in characterization of ceramic fiber structures

    NASA Astrophysics Data System (ADS)

    Järveläinen, Matti; Keskinen, Lassi; Levänen, Erkki

    2013-12-01

    Fibrous bodies that contain open porosity can have a very heterogeneous structure that is difficult to characterize in terms of local flow resistance changes within the same sample. This article presents a method that is applicable for a quick analysis of flow distribution even with large samples. In this first attempt to understand how our flow distribution thermal imaging works, we present how the measuring parameters and the results correlate with sample's thickness and density. The results indicate that our method can quickly make a distinction between areas that have different flow resistances because of variations in the sample's density or wall thickness.

  19. Structural characterization of amphiphilic homopolymer micelles using light scattering, SANS, and cryo-TEM

    PubMed Central

    Patterson, Joseph P.; Kelley, Elizabeth G.; Murphy, Ryan P.; Moughton, Adam O.; Robin, Mathew; Lu, Annhelen; Colombani, Olivier; Chassenieux, Christophe; Cheung, David; Sullivan, Millicent O.

    2013-01-01

    We report the aqueous solution self-assembly of a series of poly(N-isopropylacrylamide) (PNIPAM) polymers end-functionalized with a hydrophobic sulfur-carbon-sulfur (SCS) pincer ligand. Although the hydrophobic ligand accounted for <5 wt% of the overall homopolymer mass, the polymers self-assembled into well-defined spherical micelles in aqueous solution, and these micelles are potential precursors to solution-assembled nanoreactors for small molecule catalysis applications. The micelle structural details were investigated using light scattering, cryogenic transmission electron microscopy (cryo-TEM), and small angle neutron scattering (SANS). Radial density profiles extracted from the cryo-TEM micrographs suggested that the PNIPAM chains formed a diffuse corona with a radially decreasing corona density profile and provided valuable a priori information about the micelle structure for SANS data modeling. SANS analysis indicated a similar profile in which the corona surrounded a small hydrophobic core containing the pincer ligand. The similarity between the SANS and cryo-TEM results demonstrated that detailed information about the micelle density profile can be obtained directly from cryo-TEM and highlighted the complementary use of scattering and cryo-TEM in the structural characterization of solution-assemblies, such as the SCS pincer-functionalized homopolymers described here. PMID:24058209

  20. Structural characterization of amphiphilic homopolymer micelles using light scattering, SANS, and cryo-TEM.

    PubMed

    Patterson, Joseph P; Kelley, Elizabeth G; Murphy, Ryan P; Moughton, Adam O; Robin, Mathew; Lu, Annhelen; Colombani, Olivier; Chassenieux, Christophe; Cheung, David; Sullivan, Millicent O; Epps, Thomas H; O'Reilly, Rachel K

    2013-08-13

    We report the aqueous solution self-assembly of a series of poly(N-isopropylacrylamide) (PNIPAM) polymers end-functionalized with a hydrophobic sulfur-carbon-sulfur (SCS) pincer ligand. Although the hydrophobic ligand accounted for <5 wt% of the overall homopolymer mass, the polymers self-assembled into well-defined spherical micelles in aqueous solution, and these micelles are potential precursors to solution-assembled nanoreactors for small molecule catalysis applications. The micelle structural details were investigated using light scattering, cryogenic transmission electron microscopy (cryo-TEM), and small angle neutron scattering (SANS). Radial density profiles extracted from the cryo-TEM micrographs suggested that the PNIPAM chains formed a diffuse corona with a radially decreasing corona density profile and provided valuable a priori information about the micelle structure for SANS data modeling. SANS analysis indicated a similar profile in which the corona surrounded a small hydrophobic core containing the pincer ligand. The similarity between the SANS and cryo-TEM results demonstrated that detailed information about the micelle density profile can be obtained directly from cryo-TEM and highlighted the complementary use of scattering and cryo-TEM in the structural characterization of solution-assemblies, such as the SCS pincer-functionalized homopolymers described here.

  1. Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

    SciTech Connect

    de Serrano, Vesna; D; Antonio, Jennifer; Franzen, Stefan; Ghiladi, Reza A.

    2012-04-18

    As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 {angstrom} resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure-function relationships.

  2. Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

    SciTech Connect

    Serrano, Vesna de; D’Antonio, Jennifer; Franzen, Stefan; Ghiladi, Reza A.

    2010-05-01

    The crystal structure of dehaloperoxidase (DHP) isoenzyme B from the terebellid polychaete A. ornata, which exhibits both hemoglobin and peroxidase functions, has been determined at 1.58 Å resolution. As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 Å resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure–function relationships.

  3. [STRUCTURAL CHARACTERIZATION OF PLATELETS AND PLATELET-DERIVED MICROVESICLES].

    PubMed

    Ponomareva, A A; Nevzorova, T A; Mordakhanova, E R; Andrianova, I A; Litvinov, R I

    2016-01-01

    Platelets are the anucleated blood cells, wich together with the fibrin stop bleeding (hemostasis). Cellular microvesicles are membrane-surrounded microparticles released into extracellular space upon activation and/or apoptosis of various cells. Platelet-derived macrovesicles from the major population of circulating blood microparticles that play an important role in hemostasis and thrombosis. Despite numerous studies on the pathophysiology of platelet-derived macrovesicles, mechanisms of their formation and structural details remain poorly understood. Here we investigated the ultrastructure of parental platelets and platelet-derived microvesicles formed in vitro by quiescent cells as well as by cells stimulated with one of the following activators: arachidonic acid, ADP, thrombin, calcium ionophore A23187. Using transmission electron microscopy of human platelets and isolated microvesicles, we analyzed the intracellular origin, steps of formation, structural diversity, and size distributions of the subcellular particles. We have revealed that thrombin, unlike other stimuli, not only induced vesiculation of the plasma membrane but also caused break-up of the cells followed by formation of microparticles that are comparable with microvesicles by size. A fraction of these microparticles contained cellular organelles surrounded by a thin membrane. The size of platelet-derived macrovesicles varied from 30 nm to 500 nm, however, the size distributions depended on the nature of a cell-activating stimulus. The results obtained provide new information about the formation of platelet-derived macrovesicles and their structural diversity, wich is important to understand their multiple functions in normal and disease states.

  4. Cryo-electron tomography for structural characterization of macromolecular complexes.

    PubMed

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-08-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions.

  5. Structural and optical characterization of the propolis films

    NASA Astrophysics Data System (ADS)

    Drapak, S. I.; Bakhtinov, A. P.; Gavrylyuk, S. V.; Drapak, I. T.; Kovalyuk, Z. D.

    2006-10-01

    We have performed structural and optical characterizations of the propolis (an organic entity of biological nature) films grown on various non-organic substrates. The films were grown from a propolis melt or a propolis alcohol solution. The crystal structure has been observed in the films precipitated from the solution onto substrates such as an amorphous glass and sapphire or semiconductor indium monoselenide. For any growth method, the propolis film is a semiconductor with the bandgap of 3.07 eV at 300 K that is confirmed by a maximum in photoluminescence spectra at 2.86 eV. We argue that propolis films might be used in various optoelectronic device applications.

  6. Characterization of asphaltene structure using atomic force microscopy.

    PubMed

    Sabbaghi, S; Shariaty-Niassar, M; Ayatollahi, Sh; Jahanmiri, A

    2008-09-01

    In this study, at the first stage, asphaltene was extracted. The roughness of asphaltene coating at different rpm was studied using an image analysis confocal microscopy. The basics of quantum mechanics and statistical thermodynamics are used to predict the potential energy and the intermolecular forces of asphaltene molecules. The functional forms for the potential energy and intermolecular forces are evaluated. Our final goal is to be able to observe and determine the surface structures of asphaltene micelles with scanning probe microscopes. So, the focus of the work on these unusual molecules is to characterize their structure, dynamics and thermodynamics and to establish the relationship between these properties and petroleum fluid behaviour. The existence of various nanostructures of asphaltene in petroleum has been extensively discussed. A set of fitted data is used to check the validity of the calculated results. The good agreement between the proposed models and the data is promising.

  7. Structural characterization of carbon materials prepared at low temperature

    SciTech Connect

    Song, X.Y.; Chu, X.; Kinoshita, K.

    1995-12-31

    High-capacity carbon electrodes for rechargeable lithium-ion batteries were prepared by carbonization of thermosetting resins such as phenol-formaldehyde at temperatures between 500 C and 600 C. Their structures were characterized by high resolution transmission electron microscopy, in-situ transmission electron microscopy and x-ray diffraction analysis. These studies suggest that the carbons consist predominantly of disorganized (amorphous) phase. However evidence was found in carbon containing nickel cobalt oxide for the presence of organized graphite-like regions of parallel and curved layer planes. These graphitized structure usually appear as agglomerate particles which are composed of many smaller (100-nm diameter) particles. The high degree of graphitization is attributed to catalytic graphitization that occurs in the presence of the metal oxide.

  8. Characterization of iron-phosphate-silicate chemical garden structures.

    PubMed

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.

  9. Structural and functional characterization of two alpha-synuclein strains

    NASA Astrophysics Data System (ADS)

    Bousset, Luc; Pieri, Laura; Ruiz-Arlandis, Gemma; Gath, Julia; Jensen, Poul Henning; Habenstein, Birgit; Madiona, Karine; Olieric, Vincent; Böckmann, Anja; Meier, Beat H.; Melki, Ronald

    2013-10-01

    α-synuclein aggregation is implicated in a variety of diseases including Parkinson’s disease, dementia with Lewy bodies, pure autonomic failure and multiple system atrophy. The association of protein aggregates made of a single protein with a variety of clinical phenotypes has been explained for prion diseases by the existence of different strains that propagate through the infection pathway. Here we structurally and functionally characterize two polymorphs of α-synuclein. We present evidence that the two forms indeed fulfil the molecular criteria to be identified as two strains of α-synuclein. Specifically, we show that the two strains have different structures, levels of toxicity, and in vitro and in vivo seeding and propagation properties. Such strain differences may account for differences in disease progression in different individuals/cell types and/or types of synucleinopathies.

  10. Understanding the structure details when drying hydrate crystals of pharmaceuticals - interpretations from diffuse scattering and inter-modulation satellites of a partially dehydrated crystal.

    PubMed

    Chan, E J; Gao, Q; Dabros, M

    2014-06-01

    Simplified models for the crystal lattice of the sesquihydrate form of the hemi-sulfate salt of (5S,6S,9R)-5-amino-6-(2,3-difluorophenyl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridin-9-yl 4-(2-oxo-2,3-dihydro-1H-imidazol[4,5b]pyridin-1-yl)-1-piperidine carboxylate (BMS-927711, C28H29F2N6O3(+)) are used to calculate diffuse diffraction features in order to develop a mechanistic understanding of the dehydration process with respect to disruption of the lattice, since a Bragg model cannot be established. The model demonstrates that what we observe when the water leaves the crystal is partial transformation from the parent form to a child form (a new form, less hydrated and structurally related to the parent). Yet this `dried' structure is not a pure phase. It consists of semi-random layers of both child, parent and an interfacial layer which has a modulated structure that represents a transitory phase. Understanding the fact that a single `dried' crystal can have the disordered layer structure described as well as understanding mechanistic relationships between the phases involved can have implications in understanding the effect of common large scale bulk drying procedures. During the development of BMS-927711, difficulties did arise during characterization of the dried bulk when using only routine solid-state analysis. The material is now better understood from this diffraction study. The diffraction experiments also reveal intermodulation satellites, which upon interpretation yield even more structural information about the crystal transformation. The model suggests the mechanism of transformation is laminar in which layers of the crystal are driven to approach a stable B-centered supercell phase of lower water content.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  12. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  13. Investigation of detailed spatial structure of the Moscow urban heat island with application of the newest meteorological observations and regional climate modelling

    NASA Astrophysics Data System (ADS)

    Varentsov, Mikhail; Pavel, Konstantinov; Timofey, Samsonov

    2016-04-01

    During the last years, the network of metrological observation in Moscow megacity and its neighborhoods, forming the biggest urban agglomeration in Europe, was significantly extended. Several new weather stations and completely new dense network of air-quality monitoring appears during the last decade. In addition, several microwave meteorological profilers MTP 5, which are available to measure temperature at the heights from 0 to 1000 meters with 50-m resolution, were installed in the city and its surrounding. All these measurements allow revealing undiscovered features of Moscow urban climate and urban heat island (UHI). In our research, bases on this data, we covered several topics related to urban climatology: - Investigation of detailed spatial structure of Moscow UHI and its relationships with building features, such as land use and morphology of the street canyons, obtained by GIS-algorithms according (Samsonov et. al, 2015); - Investigation of three-dimensional structure of the UHI, including its vertical extend and influence on the stratification of the atmosphere, and three-dimensional structure of the urban heat island advection and urban heat plumes; - Application of the newest data for validation of the regional climate model COSMO-CLM, coupled with TEB urban scheme (Masson, 2000; Trusilova et. al., 2013), launched for Moscow region with 1-km spatial resolution. References: 1. Masson V. A. Physically-Based Scheme for the Urban Energy Budget in Atmospheric models. Bound. Layer Meteor. 2000. V. 94 (3). P. 357-397. 2. Trusilova K., Früh B., Brienen S., Walter A., Masson V., Pigeon G., Becker P. Implementation of an Urban Parameterization Scheme into the Regional Climate Model COSMO-CLM. J. Appl. Meteor. Climatol. V. 52. P. 2296-2311. 3. Samsonov T.E., Konstantinov P.I., Varentsov M.I. Object-oriented approach to urban canyon analysis and its applications in meteorological modeling. Urban Climate. 2015. Vol. 13. P. 122-139.

  14. Characterizing rhodopsin signaling by EPR spectroscopy: from structure to dynamics.

    PubMed

    Van Eps, Ned; Caro, Lydia N; Morizumi, Takefumi; Ernst, Oliver P

    2015-09-26

    Electron paramagnetic resonance (EPR) spectroscopy, together with spin labeling techniques, has played a major role in the characterization of rhodopsin, the photoreceptor protein and G protein-coupled receptor (GPCR) in rod cells. Two decades ago, these biophysical tools were the first to identify transmembrane helical movements in rhodopsin upon photo-activation, a critical step in the study of GPCR signaling. EPR methods were employed to identify functional loop dynamics within rhodopsin, to measure light-induced millisecond timescale changes in rhodopsin conformation, to characterize the effects of partial agonists on the apoprotein opsin, and to study lipid interactions with rhodopsin. With the emergence of advanced pulsed EPR techniques, the stage was set to determine the amplitude of structural changes in rhodopsin and the dynamics in the rhodopsin signaling complexes. Work in this area has yielded invaluable information about mechanistic properties of GPCRs. Using EPR techniques, receptors are studied in native-like membrane environments and the effects of lipids on conformational equilibria can be explored. This perspective addresses the impact of EPR methods on rhodopsin and GPCR structural biology, highlighting historical discoveries made with spin labeling techniques, and outlining exciting new directions in the field.

  15. Amyloid oligomer structure characterization from simulations: A general method

    SciTech Connect

    Nguyen, Phuong H.; Li, Mai Suan

    2014-03-07

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ{sub 9−40}, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  16. Photogrammetric detection technique for rotor blades structural characterization

    NASA Astrophysics Data System (ADS)

    Enei, C.; Bernardini, G.; Serafini, J.; Mattioni, L.; Ficuciello, C.; Vezzari, V.

    2015-11-01

    This paper describes an innovative use of photogrammetric detection techniques to experimentally estimate structural/inertial properties of helicopter rotor blades. The identification algorithms for the evaluation of mass and flexural stiffness distributions are an extension of the ones proposed by Larsen, whereas the procedure for torsional properties determination (stiffness and shear center position) is based on the Euler-Prandtl beam theory. These algorithms rely on measurements performed through photogrammetric detection, which requires the collection of digital photos allowing the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D pictures. The displacements are evaluated by comparing the positions of markers in loaded and reference configuration. Being the applied loads known, the structural characteristics can be directly obtained from the measured displacements. The accuracy of the proposed identification algorithms has been firstly verified by comparison with numerical and experimental data, and then applied to the structural characterization of two main rotor blades, designed for ultra-light helicopter applications.

  17. Cloning, expression, and preliminary structural characterization of RTN-1C

    SciTech Connect

    Fazi, Barbara; Melino, Sonia; Sano, Federica Di; Cicero, Daniel O.; Piacentini, Mauro . E-mail: mauro.piacentini@uniroma2.it; Paci, Maurizio

    2006-04-14

    Reticulons (RTNs) are endoplasmic reticulum-associated proteins widely distributed in plants, yeast, and animals. They are characterized by unique N-terminal parts and a common 200 amino acid C-terminal domain containing two long hydrophobic sequences. Despite their implication in many cellular processes, their molecular structure and function are still largely unknown. In this study, the reticulon family member RTN-1C has been expressed and purified in Escherichia coli and its molecular structure has been analysed by fluorescence and CD spectroscopy in different detergents in order to obtain a good solubility and a relative stability. The isotopically enriched protein has been also produced to perform structural studies by NMR spectroscopy. The preliminary results obtained showed that RTN-1C protein possesses helical transmembrane segments when a membrane-like environment is produced by detergents. Moreover, fluorescence experiments indicated the exposure of tryptophan side chains as predicted by structure prediction programs. We also produced the isotopically labelled protein and the procedure adopted allowed us to plan future NMR studies to investigate the biochemical behaviour of reticulon-1C and of its peptides spanning out from the membrane.

  18. Amyloid oligomer structure characterization from simulations: A general method

    NASA Astrophysics Data System (ADS)

    Nguyen, Phuong H.; Li, Mai Suan; Derreumaux, Philippe

    2014-03-01

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  19. Amyloid oligomer structure characterization from simulations: a general method.

    PubMed

    Nguyen, Phuong H; Li, Mai Suan; Derreumaux, Philippe

    2014-03-07

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  20. Size-separation characterization of starch and glycogen for biosynthesis-structure-property relationships.

    PubMed

    Gilbert, Robert G

    2011-02-01

    Starch and glycogen are highly branched polymers of glucose of great importance to humans in managing and mitigating nutrition-related diseases, especially diabetes and obesity, and in industrial uses, for example in food and paper-making. Size-separation characterization using multiple-detection size-exclusion chromatography (SEC, also known as gel-permeation chromatography, GPC) is able to furnish substantial amounts of information on the relationships between the biosynthesis, processing, structure, and properties of these biopolymers, and achieves superior characterization for use in industrial product and process improvements. Multi-detector SEC is able to give much more information about structure than simple averages such as total molecular weight or size; the detailed information yielded by this technique has already given new information on important biosynthesis-structure-property reactions, and has considerable potential in this field in the future. However, it must be used with care to avoid artifacts arising from incomplete dissolution of the substrate and shear scission during separation. It is also essential in interpreting data to appreciate that this size-separation technique can only ever give size distributions, never true molecular weight distributions. Other size-separation techniques, particularly field-flow fractionation, require substantial technical development to be used on undegraded native starches.

  1. Function Discovery and Structural Characterization of a Methylphosphonate Esterase

    SciTech Connect

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V.; Toro, Rafael; Almo, Steven C.; Raushel, Frank M.

    2015-05-12

    Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG). We also determined the structure with manganese and butyrate in the active site (PDB id: 4QSF). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. Moreover, the substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat /Km values of 580 s–1 and 1.2 × 105 M–1 s–1, respectively) and 4-nitrophenyl butyrate (kcat and kcat /Km values of 140 s–1 and 1.4 × 105 M–1 s–1, respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.

  2. The criticality of high-resolution N-linked carbohydrate assays and detailed characterization of antibody effector function in the context of biosimilar development.

    PubMed

    Brady, Lowell J; Velayudhan, Jyoti; Visone, Devi B; Daugherty, Ken C; Bartron, Jeff L; Coon, Michael; Cornwall, Cabot; Hinckley, Peter J; Connell-Crowley, Lisa

    2015-01-01

    Accurate measurement and functional characterization of antibody Fc domain N-linked glycans is critical to successful biosimilar development. Here, we describe the application of methods to accurately quantify and characterize the N-linked glycans of 2 IgG1 biosimilars with effector function activity, and show the potential pitfalls of using assays with insufficient resolution. Accurate glycan assessment was combined with glycan enrichment using lectin chromatography or production with glycosylation inhibitors to produce enriched pools of key glycan species for subsequent assessment in cell-based antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity effector function assays. This work highlights the challenges of developing high-quality biosimilar candidates and the need for modern biotechnology capabilities. These results show that high-quality analytics, combined with sensitive cell-based assays to study in vivo mechanisms of action, is an essential part of biosimilar development.

  3. Structural characterization of metal binding to a cold-adapted frataxin.

    PubMed

    Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

    2015-06-01

    Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.

  4. Characterization of Topography and Vegetation Structure using Dual-wavelength LIDAR and High-Resolution Stereo Imagery

    NASA Astrophysics Data System (ADS)

    Leigh, H. W.; Magruder, L. A.; Neuenschwander, A. L.

    2015-12-01

    This study examines the utility of co-collected, dual-wavelength, full-waveform LIDAR and high resolution stereo imagery to improve characterizations of topography and vegetation over two survey sites near Monterey, CA. Extraction of waveform features, such as total waveform energy, canopy energy distribution, and foliage penetration metrics are computed along the laser line-of-sight and along the vertical axis of synthesized "pseudowaveforms." The pseudowaveform technique is a novel method that allows for direct comparisons between green (532nm) and near IR (1064nm) waveforms, despite variations in sampling. Comparisons between wavelengths allows for detailed characterization of vegetation structure and distribution not possible with single-wavelength LIDAR. Additionally, point clouds derived from stereo imagery are fused with LIDAR point clouds to increase resolution and improve accuracy of bare earth digital elevation models, further augmenting characterization of tree height and structure.

  5. Should the reorganization of addiction-related research across all the National Institutes of Health be structural?--The devil is truly in the details.

    PubMed

    Johnson, Bankole A; Messing, Robert O; Charness, Michael E; Crabbe, John C; Goldman, Mark S; Harris, R Adron; Kranzler, Henry R; Mitchell, Mack C; Nixon, Sara Jo; Riley, Edward P; Schuckit, Marc A; Sher, Kenneth J; Thomas, Jennifer D

    2011-04-01

    The recent proposal to dissolve the National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse and create a new institute for substance use, abuse, and addiction will require significant effort by the staff of both institutes, the Advisory Councils, and outside experts to overcome complex challenges that could threaten its success. Although integration of the grants portfolios can be achieved, harmonization of goals and policies related to legal use of alcohol versus illegal consumption of drugs will present serious challenges. Consolidating the infrastructure of the 2 existing institutes would entail avoiding encroachment on grant funding. A new institute for substance use, abuse, and addiction would require an enormous amount of cooperation from other institutes as the portfolios of research on alcohol, tobacco, and other drug abuse should logically be transferred to the new institute. In the near term, a structural reorganization would be less efficient and more costly than the individual institutes are currently. Increasing efficiency and reducing costs over time will necessitate careful strategic planning. Success in this difficult task would be made easier and less costly by first implementing carefully placed building blocks of increasing functional reorganization. The newly created institute should increase opportunities for specialization within disorders of addiction, attract new leadership, and build a novel strategic plan that will energize scientists and staff and incorporate ideas of stakeholders to advance the public good in preventing and treating alcohol, tobacco, and all addictions. Attention must be paid to the devil in the details.

  6. SHOULD THE REORGANIZATION OF ADDICTION-RELATED RESEARCH ACROSS ALL THE NATIONAL INSTITUTES OF HEALTH BE STRUCTURAL?—THE DEVIL IS TRULY IN THE DETAILS

    PubMed Central

    Johnson, Bankole A.; Messing, Robert O.; Charness, Michael E.; Crabbe, John C.; Goldman, Mark S.; Harris, R. Adron; Kranzler, Henry R.; Mitchell, Mack C.; Nixon, Sara Jo; Riley, Edward P.; Schuckit, Marc A.; Sher, Kenneth J.; Thomas, Jennifer D.

    2011-01-01

    The recent proposal to dissolve the National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse and create a new institute for substance use, abuse, and addiction will require significant effort by the staff of both institutes, the Advisory Councils, and outside experts to overcome complex challenges that could threaten its success. Although integration of the grants portfolios can be achieved, harmonization of goals and policies related to legal use of alcohol versus illegal consumption of drugs will present serious challenges. Consolidating the infrastructure of the two existing institutes would entail avoiding encroachment on grant funding. A new institute for substance use, abuse, and addiction would require an enormous amount of cooperation from other institutes since the portfolios of research on alcohol, tobacco, and other drug abuse should logically be transferred to the new institute. In the near term, a structural reorganization would be less efficient and more costly than the individual institutes are currently. Increasing efficiency and reducing costs over time will necessitate careful strategic planning. Success in this difficult task would be made easier and less costly by first implementing carefully placed building blocks of increasing functional reorganization. The newly created institute should increase opportunities for specialization within disorders of addiction, attract new leadership, and build a novel strategic plan that will energize scientists and staff and incorporate ideas of stakeholders to advance the public good in preventing and treating alcohol, tobacco, and all addictions. Attention must be paid to the devil in the details. PMID:21443646

  7. A structural framework for anomalous change detection and characterization

    SciTech Connect

    Prasad, Lakshman; Theiler, James P

    2009-01-01

    We present a spatially adaptive scheme for automatically searching a pair of images of a scene for unusual and interesting changes. Our motivation is to bring into play structural aspects of image features alongside the spectral attributes used for anomalous change detection (ACD). We leverage a small but informative subset of pixels, namely edge pixels of the images, as anchor points of a Delaunay triangulation to jointly decompose the images into a set of triangular regions, called trixels, which are spectrally uniform. Such decomposition helps in image regularization by simple-function approximation on a feature-adaptive grid. Applying ACD to this trixel grid instead of pixels offers several advantages. It allows: (1) edge-preserving smoothing of images, (2) speed-up of spatial computations by significantly reducing the representation of the images, and (3) the easy recovery of structure of the detected anomalous changes by associating anomalous trixels with polygonal image features. The latter facility further enables the application of shape-theoretic criteria and algorithms to characterize the changes and recognize them as interesting or not. This incorporation of spatial information has the potential to filter out some spurious changes, such as due to parallax, shadows, and misregistration, by identifying and filtering out those that are structurally similar and spatially pervasive. Our framework supports the joint spatial and spectral analysis of images, potentially enabling the design of more robust ACD algorithms.

  8. Structural characterization of NETNES glycopeptide from Trypanosoma cruzi.

    PubMed

    Chiodi, Carla G; Verli, Hugo

    2013-05-24

    Trypanosoma cruzi is a protozoan, responsible for Chagas disease, that parasites triatomines and some vertebrates, mainly Homo sapiens. In 2010, nearly 10 million people in whole world, most from Latin America, had Chagas disease, which is an illness of high morbidity, low mortality, and serious problems of quality of life. The available treatment has high toxicity and low efficacy at chronic phase. Some of the protozoan antigenic or virulence factors include complex carbohydrate structures that, due to their uniqueness, may constitute potential selective targets for the development of new treatments. One example of such structures is NETNES, a low abundance T. cruzi glycopeptide, comprising 13 amino acid residues, one or two N-glycosylation chains, a GPI anchor and two P-glycosylations. In this context, the current work aims to obtain an atomic model for NETNES, including its glycan chains and membrane attachment, in order to contribute in the characterization of its structure and dynamics. Based on POPC and GPI models built in agreement with experimental data, our results indicate that, in the first third of the simulation, NETNES peptide is very flexible in solution, bending itself between asparagine residues and lying down on some carbohydrates and membrane, exposing amino acid residues and some other glycans, mainly terminal mannoses, to the extracellular medium, remaining in this position until the end of simulations.

  9. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.

    PubMed

    Cook, William J; Senkovich, Olga; Hernandez, Agustin; Speed, Haley; Chattopadhyay, Debasish

    2015-03-01

    The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes.

  10. Synthesis and characterization of carbon nanotube-polymer multilayer structures.

    PubMed

    Misra, Abha; Raney, Jordan R; De Nardo, Luigi; Craig, Anna E; Daraio, Chiara

    2011-10-25

    We develop lightweight, multilayer materials composed of alternating layers of poly dimethyl siloxane (PDMS) polymer and vertically aligned carbon nanotube (CNT) arrays, and characterize their mechanical response in compression. The CNT arrays used in the assembly are synthesized with graded mechanical properties along their thickness, and their use enables the creation of multilayer structures with low density (0.12-0.28 g/cm(3)). We test the mechanical response of structures composed of different numbers of CNT layers partially embedded in PDMS polymer, under quasi-static and dynamic loading. The resulting materials exhibit a hierarchical, fibrous structure with unique mechanical properties: They can sustain large compressive deformations (up to ∼0.8 strain) with a nearly complete recovery and present strain localization in selected sections of the materials. Energy absorption, as determined by the hysteresis observed in stress-strain curves, is found to be at least 3 orders of magnitude larger than that of natural and synthetic cellular materials of comparable density. Conductive bucky paper is included within the polymer interlayers. This allows the measurement of resistance variation as a function of applied stress, showing strong correlation with the observed strain localization in compression.

  11. Characterization of electronic structure of periodically strained graphene

    DOE PAGES

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; ...

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands.more » Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.« less

  12. Characterizing Fractured Rock with Geo-structural and Micro-structural Models

    NASA Astrophysics Data System (ADS)

    Dershowitz, William

    2015-04-01

    Fracture spatial structure and hydro-mechanical properties are key to the understanding of fractured rock geomechanical stability, hydrodynamics, and solute transport. This paper presents a quantitative approach to fracture characterization to provide information useful for stability and flow analysis, and for coupled flow/geomechanics. The approach presented is based on the concept of geo-structural, hydro-mechanical, and microstructural models. This approach is applicable for data collected from exposed surfaces (mapping, LiDAR, aero-magnetics), boreholes (core, optical images, and images based on resistivity and geophysical methods), and three dimensional imaging (seismic attributes and microseismics). Examples are presented comparing the results of conventional fracture characterization procedures and the recommended procedure. Fracture characterization for geo-structural fracture models is based on the idea that the geologically based fracture spatial pattern is the key, rather than individual fracture statistics. For example, while fracture intensity statistics can useful, the three dimensional fracture pattern for a bedded sedimentary rock can be better reproduced from the combination of a mechanical bedding model and a correlation between fracture spacing and bed height. In a fracture geo-structural model, the fracture spatial pattern, orientation, and intensity should be characterized in a combination of global and local coordinate systems. While some fracture sets may be oriented relative to the regional tectonics (the global coordinate system), other fracture sets are oriented relative to bedding (a local coordinate system). Fracture hydro-mechanical models define the combination of (a) conductive fractures, (b) flow-barrier fractures, (c) fractures which provide storage porosity, (d) fractures of significance for kinematic stability, and (e) fractures of significance for rock mass strength and deformability. The hydromechanical fractures are a subset of

  13. Tensile Characterization of FRP Rods for Reinforced Concrete Structures

    NASA Astrophysics Data System (ADS)

    Micelli, F.; Nanni, A.

    2003-07-01

    The application of FRP rods as an internal or external reinforcement in new or damaged concrete structures is based on the development of design equations that take into account the mechanical properties of FRP material systems.The measurement of mechanical characteristics of FRP requires a special anchoring and protocol, since it is well known that these characteristics depend on the direction and content of fibers. In this study, an effective tensile test method is described for the mechanical characterization of FRP rods. Twelve types of glass and carbon FRP specimens with different sizes and surface characteristics were tested to validate the procedure proposed. In all, 79 tensile tests were performed, and the results obtained are discussed in this paper. Recommendations are given for specimen preparation and test setup in order to facilitate the further investigation and standardization of the FRP rods used in civil engineering.

  14. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase.

    PubMed

    Romero, Elvira; Castellanos, J Rubén Gómez; Mattevi, Andrea; Fraaije, Marco W

    2016-12-19

    Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio-, chemo-, and enantioselectivity. However, the low stability of many Baeyer-Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate-binding cavity explains its preference for small rather than bulky substrates. Small-scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology.

  15. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase

    PubMed Central

    Romero, Elvira; Castellanos, J. Rubén Gómez

    2016-01-01

    Abstract Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio‐, chemo‐, and enantioselectivity. However, the low stability of many Baeyer–Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate‐binding cavity explains its preference for small rather than bulky substrates. Small‐scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology. PMID:27873437

  16. Characterization of Thermal and Mechanical Impact on Aluminum Honeycomb Structures

    NASA Technical Reports Server (NTRS)

    Robinson, Christen M.

    2013-01-01

    This study supports NASA Kennedy Space Center's research in the area of intelligent thermal management systems and multifunctional thermal systems. This project addresses the evaluation of the mechanical and thermal properties of metallic cellular solid (MCS) materials; those that are lightweight; high strength, tunable, multifunctional and affordable. A portion of the work includes understanding the mechanical properties of honeycomb structured cellular solids upon impact testing under ambient, water-immersed, liquid nitrogen-cooled, and liquid nitrogen-immersed conditions. Additionally, this study will address characterization techniques of the aluminum honeycomb's ability to resist multiple high-rate loadings or impacts in varying environmental conditions, using various techniques for the quantitative and qualitative determination for commercial applicability.

  17. Structural and functional characterization of enamel pigmentation in shrews.

    PubMed

    Dumont, M; Tütken, T; Kostka, A; Duarte, M J; Borodin, S

    2014-04-01

    Pigmented tooth enamel occurs in several vertebrate clades, ranging from mammals to fish. Although an iron compound is associated with this orange to red colored pigmentation, its chemical and structural organization within the enamel is unknown. To determine the nature of the iron compound, we investigated heavily pigmented teeth of the northern short-tailed shrew Blarina brevicauda using combined characterization techniques such as scanning and transmission electron microscopy and synchrotron X-ray diffraction. We found that the pigmentation of the enamel with an iron content of around 8wt% results from a close to amorphous magnetite phase deposited around the nm-sized enamel crystals. Furthermore, the influence of the pigmentation on the enamel hardness was determined by nanoindentation measurements. Finally, the biomechanical function and biological context are discussed in light of the obtained results.

  18. Hexamethylenetetramine carboxyborane: synthesis, structural characterization and CO releasing properties.

    PubMed

    Ayudhya, T I; Raymond, C C; Dingra, N N

    2017-01-17

    Carbon monoxide, although widely known as a toxic gas, has received great attention in the past few decades due to its promising role as a medical gas. Several classes of carbon monoxide releasing molecules (CORMs) have been synthesised with many of them having pharmacological activities under physiological conditions. Herein, we report the synthesis and structural characterization of the first example of amine carboxyborane that releases CO under physiological conditions without the aid of inducers. A representative compound hexamethylenetetramine carboxyborane (HMTA-CB) described here has a half-life of 2.7 days and gradually releases CO with the rate constant of 3.0 × 10(-6) s(-1). Its ability to promote cell growth shows the beneficial effect of slow CO release to supplement CO in small amounts over time.

  19. Fabrication, characterization, and application of microresonators and resonant structures

    NASA Astrophysics Data System (ADS)

    Cohoon, Gregory A.

    Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1--2 microm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10 8 and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high a 2x106. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2--5 microm and

  20. Low tip damage AFM technique development for nano structures characterization

    NASA Astrophysics Data System (ADS)

    Liu, Biao; Wang, Charles C.; Huang, Po-Fu; Uritsky, Yuri

    2010-06-01

    Ambient dynamic mode (tapping mode or intermittent-contact mode) AFM imaging has been used extensively for the characterization of the topography of nano structures. However, the results are beset with artifacts, because hard tapping of the AFM tip on sample surface usually causes premature tip damage. Through careful study of the cantilever amplitude and phase signals as functions of tip-to-sample distance, principle of non-contact AFM operation was discovered to enable high resolution and low tip damage AFM image acquisition [1, 2]. However, current study discovers that the conventional way of acquiring amplitude and phase versus distance curves gives erroneous non-contact operating range, because the tip gets damaged during the data acquisition process. A new technique is developed to reliably map the operating parameters of an intact tip that ensures the AFM be operated with the correct non-contact settings. Two examples are given to illustrate the successful applications of this new technique. The first example involves the size characterization of polystyrene latex (PSL) nano particles used for light scattering tool calibration. The second example is the development of robust recipes for the measurement of the depth of phase-shift mask trenches.

  1. Geological Features and Crustal Structure of the Cretaceous Middle Benue Trough, Nigeria: Insights from Detailed Analysis and Modelling of Magnetic and Gravity Data

    NASA Astrophysics Data System (ADS)

    Anudu, G. K.; Stephenson, R.; Macdonald, D.

    2015-12-01

    The middle Benue Trough is the middle (central) segment of the Nigerian Benue Trough, an intra-continental rift that developed during the second phase of rifting of the Gondwana supercontinent that resulted in the opening of the South Atlantic Ocean, Gulf of Guinea and separation of South America from Africa in the Late Jurassic to Early Cretaceous. Airborne magnetic and terrestrial gravity data from the area have been analysed and modelled in detail. Results obtained using a variety of edge enhancement (derivative) methods applied to high-resolution, airborne magnetic data reveal widespread magmatic intrusions (mainly volcanic/sub-volcanic rocks, with an areal extent greater than 12000 km2) and numerous geological structures. Rose (azimuth frequency) plots show that the geological structural trends are predominantly NE - SW, NW - SE and ESE - WNW with minor ENE -WSW/N - S trends and thus suggest that the area has undergone several phases of tectonic deformation at different geological times. Integrated two-dimensional (2-D) gravity and magnetic modelling along five profiles constrained by 2-D magnetic depth-to-source estimates and available seismological velocity models indicates the presence of a number of distinct crustal bodies and thin crust. Moho depth varies from ca. 21 - 29 km, while the crustal thickness ranges between ca. 19 and 29 km. Shallower Moho and thinner crust are observed along the trough axis. Results from the study also reveal that the amount of crustal thinning and crustal stretching factor (β) across the area varies from 3.3 - 14.5 km and 1.11 - 1.78, respectively. Broad positive to near positive Bouguer gravity anomalies in the region of the trough axis are due to the combined effects of dense (intermediate to basic) magmatic intrusions (both intra-sedimentary and intra-basement/crustal ones), shallow basement horsts (basement uplift zones) and thin crust replaced by dense abnormal upper mantle bodies. Reactivated intra-basement structures

  2. Perovskite oxide nanowires: synthesis, property and structural characterization.

    PubMed

    Zhu, Xinhua; Liu, Zhiguo; Ming, Naiben

    2010-07-01

    Perovskite oxide materials display a wide spectrum of functional properties, including switchable polarization, piezoelectricity, pyroelectricity, and non-linear dielectric behavior. These properties are indispensable for application in electronic devices such as non-volatile memories, sensors, microactuators, infrared detectors, microwave phase filters, and so on. Recent advances in science and technology of perovskite oxide materials have resulted in the feature sizes of perovskite oxides-based electronic devices entering into nanoscale dimensions. At nanoscale perovskite oxide materials exhibit a pronounced size effect manifesting itself in a significant deviation of the properties of low-dimensional structures from the bulk and film counterparts. In the last decade low-dimensional perovskite nanosized oxides have been received much attention because of their superior physical and chemical properties. Among them, perovskite oxide nanowires are especially attractive for nanoscience studies and nanotechnology applications. Compared to other low-dimensional perovskite oxide systems, perovskite oxide nanowires are not only used as the building blocks of future nanodevices, but also they offer fundamental scientific opportunities for investigating the intrinsic size effects of physical properties. In the recent years, much progress has been made both in synthesis and physical property testing of perovskite oxide nanowires, which have a profound impact on the nanoelectronics. In this work, an overview of the state of art in perovskite oxide nanowires is presented, which covers their synthesis, property, and structural characterization. In the first part, the recent literatures for fabricating perovskite oxide nanowires with promising features, are critically reviewed. The second part deals with the recent advances on the physical property testing of perovskite oxide nanowires. The third part summarizes the recent progress on microstructural characterizations of

  3. Structural Characterization of Myotoxic Ecarpholin S From Echis carinatus Venom

    SciTech Connect

    Zhou, X.; Tan, T; Valiyaveettil, S; Go, M; Kini, R; Velazquez-Campoy, A; Sivaraman, J

    2008-01-01

    Phospholipase A2 (PLA2), a common toxic component of snake venom, has been implicated in various pharmacological effects. Ecarpholin S, isolated from the venom of the snake Echis carinatus sochureki, is a phospholipase A2 (PLA2) belonging to the Ser49-PLA2 subgroup. It has been characterized as having low enzymatic but potent myotoxic activities. The crystal structures of native ecarpholin S and its complexes with lauric acid, and its inhibitor suramin, were elucidated. This is the first report of the structure of a member of the Ser49-PLA2 subgroup. We also examined interactions of ecarpholin S with phosphatidylglycerol and lauric acid, using surface plasmon resonance, and of suramin with isothermal titration calorimetry. Most Ca2+-dependent PLA2 enzymes have Asp in position 49, which plays a crucial role in Ca2+ binding. The three-dimensional structure of ecarpholin S reveals a unique conformation of the Ca2+-binding loop that is not favorable for Ca2+ coordination. Furthermore, the endogenously bound fatty acid (lauric acid) in the hydrophobic channel may also interrupt the catalytic cycle. These two observations may account for the low enzymatic activity of ecarpholin S, despite full retention of the catalytic machinery. These observations may also be applicable to other non-Asp49-PLA2 enzymes. The interaction of suramin in its complex with ecarpholin S is quite different from that reported for the Lys49-PLA2/suramin complex, where the interfacial recognition face (i-face), C-terminal region, and N-terminal region of ecarpholin S play important roles. This study provides significant structural and functional insights into the myotoxic activity of ecarpholin S and, in general, of non-Asp49-PLA2 enzymes.

  4. Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

    NASA Astrophysics Data System (ADS)

    Formoso, Elena; Limongelli, Vittorio; Parrinello, Michele

    2015-02-01

    Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

  5. Sizing Single Cantilever Beam Specimens for Characterizing Facesheet/Core Peel Debonding in Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.

    2010-01-01

    This paper details part of an effort focused on the development of a standardized facesheet/core peel debonding test procedure. The purpose of the test is to characterize facesheet/core peel in sandwich structure, accomplished through the measurement of the critical strain energy release rate associated with the debonding process. The specific test method selected for the standardized test procedure utilizes a single cantilever beam (SCB) specimen configuration. The objective of the current work is to develop a method for establishing SCB specimen dimensions. This is achieved by imposing specific limitations on specimen dimensions, with the objectives of promoting a linear elastic specimen response, and simplifying the data reduction method required for computing the critical strain energy release rate associated with debonding. The sizing method is also designed to be suitable for incorporation into a standardized test protocol. Preliminary application of the resulting sizing method yields practical specimen dimensions.

  6. 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

  7. Development of an in-situ soil structure characterization methodology

    NASA Astrophysics Data System (ADS)

    Debos, Endre; Kriston, Sandor

    2015-04-01

    The agricultural cultivation has several direct and indirect effects on the soil properties, among which the soil structure degradation is the best known and most detectable one. Soil structure degradation leads to several water and nutrient management problems, which reduce the efficiency of agricultural production. There are several innovative technological approaches aiming to reduce these negative impacts on the soil structure. The tests, validation and optimization of these methods require an adequate technology to measure the impacts on the complex soil system. This study aims to develop an in-situ soil structure and root development testing methodology, which can be used in field experiments and which allows one to follow the real time changes in the soil structure - evolution / degradation and its quantitative characterization. The method is adapted from remote sensing image processing technology. A specifically transformed A/4 size scanner is placed into the soil into a safe depth that cannot be reached by the agrotechnical treatments. Only the scanner USB cable comes to the surface to allow the image acquisition without any soil disturbance. Several images from the same place can be taken throughout the vegetation season to follow the soil consolidation and structure development after the last tillage treatment for the seedbed preparation. The scanned image of the soil profile is classified using supervised image classification, namely the maximum likelihood classification algorithm. The resulting image has two principal classes, soil matrix and pore space and other complementary classes to cover the occurring thematic classes, like roots, stones. The calculated data is calibrated with filed sampled porosity data. As the scanner is buried under the soil with no changes in light conditions, the image processing can be automated for better temporal comparison. Besides the total porosity each pore size fractions and their distributions can be calculated for

  8. Characterizing the structure and content of nurse handoffs: A Sequential Conversational Analysis approach.

    PubMed

    Abraham, Joanna; Kannampallil, Thomas; Brenner, Corinne; Lopez, Karen D; Almoosa, Khalid F; Patel, Bela; Patel, Vimla L

    2016-02-01

    Effective communication during nurse handoffs is instrumental in ensuring safe and quality patient care. Much of the prior research on nurse handoffs has utilized retrospective methods such as interviews, surveys and questionnaires. While extremely useful, an in-depth understanding of the structure and content of conversations, and the inherent relationships within the content is paramount to designing effective nurse handoff interventions. In this paper, we present a methodological framework-Sequential Conversational Analysis (SCA)-a mixed-method approach that integrates qualitative conversational analysis with quantitative sequential pattern analysis. We describe the SCA approach and provide a detailed example as a proof of concept of its use for the analysis of nurse handoff communication in a medical intensive care unit. This novel approach allows us to characterize the conversational structure, clinical content, disruptions in the conversation, and the inherently phasic nature of nurse handoff communication. The characterization of communication patterns highlights the relationships underlying the verbal content of nurse handoffs with specific emphasis on: the interactive nature of conversation, relevance of role-based (incoming, outgoing) communication requirements, clinical content focus on critical patient-related events, and discussion of pending patient management tasks. We also discuss the applicability of the SCA approach as a method for providing in-depth understanding of the dynamics of communication in other settings and domains.

  9. Characterization of carbonized polydopamine nanoparticles suggests ordered supramolecular structure of polydopamine.

    PubMed

    Yu, Xiang; Fan, Hailong; Liu, Yang; Shi, Zujin; Jin, Zhaoxia

    2014-05-20

    Polydopamine is not only a multifunctional biopolymer with promising optoelectronic properties but it is also a versatile coating platform for different surfaces. The structure and formation of polydopamine is an active area of research. Some studies have supposed that polydopamine is composed of covalently bonded dihydroxyindole, indoledione, and dopamine units, but others proposed that noncovalent self-assembly contributes to polydopamine formation as well. However, it is difficult to directly find the details of supramolecular structure of polydopamine via self-assembly. In this study, we first report the graphite-like nanostructure observed in the carbonized polydopamine nanoparticles in nitrogen (or argon) environment at 800 °C. Raman characterization, which presents the typical D band and G band, confirmed the existence of graphite-like nanostructures. Our observation provides clear evidence for a layered-stacking supramolecular structure of polydopamine. Particularly, the size of graphite-like domains is similar to that of disk-shaped aggregates hypothesized in previous study about the polymerization of 5,6-dihydroxyindole [ Biomacromolecules 2012 , 13 , 2379 ]. Analysis of the hierarchical structure of polydopamine helps us understand its formation.

  10. Biochemical and structural characterization of a novel bacterial manganese-dependent hydroxynitrile lyase.

    PubMed

    Hajnal, Ivan; Lyskowski, Andrzej; Hanefeld, Ulf; Gruber, Karl; Schwab, Helmut; Steiner, Kerstin

    2013-11-01

    Hydroxynitrile lyases (HNLs), which catalyse the decomposition of cyanohydrins, are found mainly in plants. In vitro, they are able to catalyse the synthesis of enantiopure cyanohydrins, which are versatile building blocks in the chemical industry. Recently, HNLs have also been discovered in bacteria. Here, we report on the detailed biochemical and structural characterization of a hydroxynitrile lyase from Granulicella tundricola (GtHNL), which was successfully heterologously expressed in Escherichia coli. The crystal structure was solved at a crystallographic resolution of 2.5 Å and exhibits a cupin fold. As GtHNL does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs, cupins represent a new class of HNLs. GtHNL is metal-dependent, as confirmed by inductively coupled plasma/optical emission spectroscopy, and in the crystal structure, manganese is bound to three histidine and one glutamine residue. GtHNL displayed a specific activity of 1.74 U·mg(-1) at pH 6 with (R)-mandelonitrile, and synthesized (R)-mandelonitrile with 90% enantiomeric excess at 80% conversion using 0.5 m benzaldehyde in a biphasic reaction system with methyl tertiary butyl ether.

  11. Deployment, Foam Rigidization, and Structural Characterization of Inflatable Thin-Film Booms

    NASA Technical Reports Server (NTRS)

    Schnell, Andrew R.; Leigh, Larry M., Jr.; Tinker, Michael L.; McConnaughey, Paul R. (Technical Monitor)

    2002-01-01

    Detailed investigation of the construction, packaging/deployment, foam rigidization, and structural characterization of polyimide film inflatable booms is described. These structures have considerable potential for use in space with solar concentrators, solar sails, space power systems including solar arrays, and other future missions. Numerous thin-film booms or struts were successfully constructed, inflated, injected with foam, and rigidized. Both solid-section and annular test articles were fabricated, using Kapton polyimide film, various adhesives, Styrofoam end plugs, and polyurethane pressurized foam. Numerous inflation/deployment experiments were conducted and compared to computer simulations using the MSC/DYTRAN code. Finite element models were developed for several foam-rigidized struts and compared to model test results. Several problems encountered in the construction, deployment, and foam injection/rigidization process are described. Areas of difficulty included inadequate adhesive strength, cracking of the film arid leakage, excessive bending of the structure during deployment, problems with foam distribution and curing properties, and control of foam leakage following injection into the structure. Many of these problems were overcome in the course of the research.

  12. Structural characterization of Turtle Mountain anticline (Alberta, Canada) and impact on rock slope failure

    NASA Astrophysics Data System (ADS)

    Humair, Florian; Pedrazzini, Andrea; Epard, Jean-Luc; Froese, Corey R.; Jaboyedoff, Michel

    2013-10-01

    This paper proposes a structural investigation of the Turtle Mountain anticline (Alberta, Canada) to better understand the role of the different tectonic features on the development of both local and large scale rock slope instabilities occurring in Turtle Mountain. The study area is investigated by combining remote methods with detailed field surveys. In particular, the benefit of Terrestrial Laser Scanning for ductile and brittle tectonic structure interpretations is illustrated. The proposed tectonic interpretation allows the characterization of the fracturing pattern, the fold geometry and the role of these tectonic features in rock slope instability development. Ten discontinuity sets are identified in the study area, their local variations permitting the differentiation of the study zone into 20 homogenous structural domains. The anticline is described as an eastern verging fold that displays considerable geometry differences along its axis and developed by both flexural slip and tangential longitudinal strain folding mechanisms. Moreover, the origins of the discontinuity sets are determined according to the tectonic phases affecting the region (pre-folding, folding, post-folding). The localization and interpretation of kinematics of the different instabilities revealed the importance of considering the discrete brittle planes of weakness, which largely control the kinematic release of the local instabilities, and also the rock mass damage induced by large tectonic structures (fold hinge, thrust).

  13. Characterization and estimation of permeability correlation structure from performance data

    SciTech Connect

    Ershaghi, I.; Al-Qahtani, M.

    1997-08-01

    In this study, the influence of permeability structure and correlation length on the system effective permeability and recovery factors of 2-D cross-sectional reservoir models, under waterflood, is investigated. Reservoirs with identical statistical representation of permeability attributes are shown to exhibit different system effective permeability and production characteristics which can be expressed by a mean and variance. The mean and variance are shown to be significantly influenced by the correlation length. Detailed quantification of the influence of horizontal and vertical correlation lengths for different permeability distributions is presented. The effect of capillary pressure, P{sub c1} on the production characteristics and saturation profiles at different correlation lengths is also investigated. It is observed that neglecting P{sub c} causes considerable error at large horizontal and short vertical correlation lengths. The effect of using constant as opposed to variable relative permeability attributes is also investigated at different correlation lengths. Next we studied the influence of correlation anisotropy in 2-D reservoir models. For a reservoir under five-spot waterflood pattern, it is shown that the ratios of breakthrough times and recovery factors of the wells in each direction of correlation are greatly influenced by the degree of anisotropy. In fully developed fields, performance data can aid in the recognition of reservoir anisotropy. Finally, a procedure for estimating the spatial correlation length from performance data is presented. Both the production performance data and the system`s effective permeability are required in estimating the correlation length.

  14. Processing-structure characterization of rheocast IN-100 superalloy

    NASA Astrophysics Data System (ADS)

    Cheng, Jung-Jen Allen; Apelian, Diran; Doherty, Roger D.

    1986-11-01

    The rheocasting solidification process has been applied in the production of IN-100 nickel base superalloy. A high vacuum furnace for rheocasting superalloys was used to rheocast ingots under different processing conditions. Processing variables which were evaluated include stirring speed, isothermal stirring time, and volume fraction solid during isothermal stirring. Ingots, furnace cooled at the same rate but without stirring, were also examined for comparison with the rheocast ingots. A detailed microstructural examination was made of the resultant microstructure both on furnace cooling after stirring and on reheating to the isothermal stirring temperature followed by water quenching. Rheocasting yielded fine-grained structures, where the extent of microsegregatiori, the variation in macrostructure, and the solidification-induced porosity were found to be reduced in comparison to the unstirred ingot. The grain size and nonuniformity in the as-cast ingot were reduced by increasing the stirring speed, isothermal stirring time, or the volume fraction solid during stirring. The degree of the microsegregation decreased significantly with increasing volume fraction solid. Grain boundaries, both with and without solute enrichment, were found in the rosette-like solid particles after rheocasting, lending support to the Vogel-Cantor-Doherty model of rheocasting based on the formation of grain boundaries by strain-induced recrystallization and by sintering. It is clear from these results that the microstructure of this superalloy was significantly improved by rheocasting. Improved mechanical properties were also found and will be reported separately.

  15. Characterization of 32nm node BEOL grating structures using scatterometry

    NASA Astrophysics Data System (ADS)

    Zangooie, Shahin; Sendelbach, Matthew; Angyal, Matthew; Archie, Charles; Vaid, Alok; Matthew, Itty; Herrera, Pedro

    2008-03-01

    Implementations of scatterometry in the back end of the line (BEOL) of the devices requires design of advanced measurement targets with attention to CMP ground rule constraints as well as model simplicity details. In this paper we outline basic design rules for scatterometry back end targets by stacking and staggering measurement pads to reduce metal pattern density in the horizontal plane of the device and to avoid progressive dishing problems along the vertical direction. Furthermore, important characteristics of the copper shapes in terms of their opaqueness and uniformity are discussed. It is shown that the M1 copper thicknesses larger than 100 nm are more than sufficient for accurate back end scatterometry implementations eliminating the need for modeling of contributions from the buried layers. AFM and ellipsometry line scans also show that the copper pads are sufficiently uniform with a sweet spot area of around 20 μm. Hence, accurate scatterometry can be done with negligible edge and/or dishing contributions if the measurement spot is placed any where within the sweet spot area. Reference metrology utilizing CD-SEM and CD-AFM techniques prove accuracy of the optical solutions for the develop inspect and final inspect grating structures. The total measurement uncertainty (TMU) values for the process of record line width are of the order of 0.77 nm and 0.35 nm at the develop inspect and final inspect levels, respectively.

  16. Structural characterization of a serendipitously discovered bioactive macromolecule, lignin sulfate.

    PubMed

    Raghuraman, Arjun; Tiwari, Vaibhav; Thakkar, Jay N; Gunnarsson, Gunnar T; Shukla, Deepak; Hindle, Michael; Desai, Umesh R

    2005-01-01

    The herpes simplex virus-1 (HSV-1) utilizes cell-surface glycosaminoglycan, heparan sulfate, to gain entry into cells and cause infection. In a search for synthetic mimics of heparan sulfate to prevent HSV infection, we discovered potent inhibitory activity arising from sulfation of a monomeric flavonoid. Yet, detailed screening indicated that the sulfated flavonoid was completely inactive and the potent inhibitory activity arose from a macromolecular substance present in the parent flavonoid. The active principle was identified through a battery of biophysical and chemical analyses as a sulfated form of lignin, a three-dimensional network polymer composed of substituted phenylpropanoid monomers. Mass spectral analysis of the parent lignin and its sulfated derivative indicates the presence of p-coumaryl monomers interconnected through uncondensed beta-O-4-linkages. Elemental analysis of lignin sulfate correlates primarily with a polymer of p-coumaryl alcohol containing one sulfate group. High-performance size exclusion chromatography shows a wide molecular weight distribution from 1.5 to 40 kDa suggesting significant polydispersity. Polyacrylamide gel electrophoresis (PAGE) analysis indicates a highly networked polymer that differs significantly from linear charged polymers with respect to its electrophoretic mobility. Overall, macromolecular lignin sulfate presents a multitude of substructures that can interact with biomolecules, including viral glycoproteins, using hydrophobic, hydrogen-bonding, and ionic forces. Thus, lignin sulfate represents a large number of interesting structures with potential medicinal benefits.

  17. Structural characterization of glycosaminoglycans from zebrafish in different ages

    PubMed Central

    Zhang, Fuming; Zhang, Zhenqing; Thistle, Robert; McKeen, Lindsey; Hosoyama, Saori; Toida, Toshihiko

    2009-01-01

    The zebrafish (Danio rerio) is a popular model organism for the study of developmental biology, disease mechanisms, and drug discovery. Glycosaminoglycans (GAGs), located on animal cell membranes and in the extracellular matrix, are important molecules in cellular communication during development, in normal physiology and pathophysiology. Vertebrates commonly contain a variety of GAGs including chondroitin/dermatan sulfates, heparin/heparan sulfate, hyaluronan and keratan sulfate. Zebrafish might represent an excellent experimental organism to study the biological roles of GAGs. A recent study showing the absence of heparan sulfate in adult zebrafish, suggested a more detailed evaluation of the GAGs present in this important model organism needed to be undertaken. This report aimed at examining the structural alterations of different GAGs at the molecular level at different developmental stages. GAGs were isolated and purified from zebrafish in different stages in development ranging from 0.5 days to adult. The content and disaccharide composition of chondroitin sulfate and heparan sulfate were determined using chemical assays, liquid chromotography and mass spectrometry. The presence of HS in adult fish was also confirmed using 1H-NMR. PMID:18777207

  18. Production and Structural Characterization of Lactobacillus helveticus Derived Biosurfactant

    PubMed Central

    Sharma, Deepansh; Saharan, Baljeet Singh; Chauhan, Nikhil; Bansal, Anshul; Procha, Suresh

    2014-01-01

    A probiotic strain of lactobacilli was isolated from traditional soft Churpi cheese of Yak milk and found positive for biosurfactant production. Lactobacilli reduced the surface tension of phosphate buffer saline (PBS) from 72.0 to 39.5 mNm−1 pH 7.2 and its critical micelle concentration (CMC) was found to be 2.5 mg mL−1. Low cost production of Lactobacilli derived biosurfactant was carried out at lab scale fermenter which yields 0.8 mg mL−1 biosurfactant. The biosurfactant was found least phytotoxic and cytotoxic as compared to the rhamnolipid and sodium dodecyl sulphate (SDS) at different concentration. Structural attributes of biosurfactant were determined by FTIR, NMR (1H and 13C), UPLC-MS, and fatty acid analysis by GCMS which confirmed the presence of glycolipid type of biosurfactant closely similar to xylolipids. Biosurfactant is mainly constituted by lipid and sugar fractions. The present study outcomes provide valuable information on structural characterization of the biosurfactant produced by L. helveticus MRTL91. These findings are encouraging for the application of Lactobacilli derived biosurfactant as nontoxic surface active agents in the emerging field of biomedical applications. PMID:25506070

  19. Structural characterization of mesquite (Prosopis velutina) gum and its fractions.

    PubMed

    López-Franco, Yolanda L; de la Barca, Ana M Calderón; Valdez, Miguel A; Peter, Martin G; Rinaudo, Marguerite; Chambat, Gérard; Goycoolea, Francisco M

    2008-08-11

    Structural and physicochemical characteristics of mesquite gum (from Prosopis velutina) were investigated using FT-IR spectroscopic, mass spectrometric and chromatographic methods. Four fractions (F-I, F-IIa, F-IIb and F-III) were isolated by hydrophobic interaction chromatography. The samples were characterized and analyzed for their monosaccharide and oligomers composition by high performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). L-Arabinose (L-Ara) and D-galactose (D-Gal) were found as the main carbohydrate constituent residues in the polysaccharides from mesquite gum and their ratio (L-Ara/D-Gal) varied within the range 2.54 to 3.06 among the various fractions. Small amounts of D-glucose (D-Glc), D-mannose (D-Man) and D-xylose (D-Xyl) were also detected, particularly in Fractions IIa, IIb and III. Infrared spectroscopy identified polysaccharides and protein in all the samples. Data from mass spectrometry (MALDI-TOF MS) was consistent with the idea that the structure corresponding to the periphereal chains of Fraction I is predominantly a chain of pentoses attached to uronic acid.

  20. Microstructural, Structural, and Thermal Characterization of Annealed Carbon Steels

    NASA Astrophysics Data System (ADS)

    Lara-Guevara, A.; Ortiz-Echeverri, C. J.; Rojas-Rodriguez, I.; Mosquera-Mosquera, J. C.; Ariza-Calderón, H.; Ayala-Garcia, I.; Rodriguez-García, M. E.

    2016-10-01

    As is well known, the metallurgical microstructure of carbon steel is formed by ferrite and pearlite after the annealing heat treatment. When the cooling rate increases, the diffusive process is interrupted causing a change in the metallurgical microstructure which will affect steel properties. The aim of this work was to study thermal, structural, and microstructural properties of annealed carbon steel samples with four different carbon contents. Crystalline structure and crystalline quality were studied by the X-ray diffraction technique, where the full width at half maximum analysis showed that as the carbon content increased, the crystalline quality decreased. The metallurgical microstructure morphology was studied by scanning electron microscopy. The thermal diffusivity and the heat capacity were determined by the photoacoustic technique and by the thermal relaxation method, respectively. The thermal diffusivity and the thermal conductivity decreased as the carbon content increased. The amplitude signal of photothermal radiometry increased as the carbon content increased, while the phase signal of photothermal radiometry did not show significant differences among studied carbon steel types. The photoacoustic technique represents an important alternative in the steel characterization field.

  1. Microstructural characterization and pore structure analysis of nuclear graphite

    NASA Astrophysics Data System (ADS)

    Kane, J.; Karthik, C.; Butt, D. P.; Windes, W. E.; Ubic, R.

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between ˜14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of ˜2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  2. Microstructural Characterization and Pore Structure Analysis of Nuclear Graphite

    SciTech Connect

    J. Kane; C. Karthik; D. P. Butt; W. E. Windes; R. Ubic

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between {approx}14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of {approx}2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  3. Characterization of large structural genetic mosaicism in human autosomes.

    PubMed

    Machiela, Mitchell J; Zhou, Weiyin; Sampson, Joshua N; Dean, Michael C; Jacobs, Kevin B; Black, Amanda; Brinton, Louise A; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M; Gaudet, Mia M; Haiman, Christopher A; Hankinson, Susan E; Hartge, Patricia; Henderson, Brian E; Hong, Yun-Chul; Hosgood, H Dean; Hsiung, Chao A; Hu, Wei; Hunter, David J; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M; Matsuo, Keitaro; Olson, Sara H; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C; Albanes, Demetrius; Aldrich, Melinda C; Amos, Christopher; Amundadottir, Laufey T; Berndt, Sonja I; Blot, William J; Bock, Cathryn H; Bracci, Paige M; Burdett, Laurie; Buring, Julie E; Butler, Mary A; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C; Cook, Michael B; Cullen, Michael; Davis, Faith G; Ding, Ti; Duell, Eric J; Epstein, Caroline G; Fan, Jin-Hu; Figueroa, Jonine D; Fraumeni, Joseph F; Freedman, Neal D; Fuchs, Charles S; Gao, Yu-Tang; Gapstur, Susan M; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J Michael; Giles, Graham G; Gillanders, Elizabeth M; Giovannucci, Edward L; Goldin, Lynn; Goldstein, Alisa M; Greene, Mark H; Hallmans, Goran; Harris, Curtis C; Henriksson, Roger; Holly, Elizabeth A; Hoover, Robert N; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M; Malats, Nuria; McGlynn, Katherine A; McNeill, Lorna H; McWilliams, Robert R; Melin, Beatrice S; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G; Rajaraman, Preetha; Real, Francisco X; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M; Savage, Sharon A; Schwartz, Ann G; Schwartz, Kendra L; Sesso, Howard D; Severi, Gianluca; Silverman, Debra T; Spitz, Margaret R; Stevens, Victoria L; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R; Teras, Lauren R; Tobias, Geoffrey S; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J; Wheeler, William; White, Emily; Wiencke, John K; Wolpin, Brian M; Wu, Xifeng; Wunder, Jay S; Yu, Kai; Zanetti, Krista A; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G; de Andrade, Mariza; Barnes, Kathleen C; Beaty, Terri H; Bierut, Laura J; Desch, Karl C; Doheny, Kimberly F; Feenstra, Bjarke; Ginsburg, David; Heit, John A; Kang, Jae H; Laurie, Cecilia A; Li, Jun Z; Lowe, William L; Marazita, Mary L; Melbye, Mads; Mirel, Daniel B; Murray, Jeffrey C; Nelson, Sarah C; Pasquale, Louis R; Rice, Kenneth; Wiggs, Janey L; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A; Laurie, Cathy C; Caporaso, Neil E; Yeager, Meredith; Chanock, Stephen J

    2015-03-05

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.

  4. Structural characterization of phytotoxic terpenoids from Cestrum parqui.

    PubMed

    D'Abrosca, Brigida; Dellagreca, Marina; Fiorentino, Antonio; Monaco, Pietro; Natale, Angela; Oriano, Palma; Zarrelli, Armando

    2005-11-01

    Isolation, chemical characterization and phytotoxicity of nine polyhydroxylated terpenes (five C13nor-isoprenoids, two sesquiterpenes, a spirostane and a pseudosapogenin) from Cestrum parqui L'Herr are reported. In this work we completed the phytochemical investigation of the terpenic fraction of the plant and described the structural elucidation of polar isoprenoids using NMR methods. All the configurations of the compounds have been assigned by NOESY experiments. Four new structures have been identified as (3S,5R,6R,7E,9R)-5,6,9-trihydroxy-3-isopropyloxy-7-megastigmene, 5alpha-spirostan-3beta,12beta,15alpha-triol, and 26-O-(3'-isopentanoyl)-beta-d-glucopyranosyl-5alpha-furost-20(22)-ene-3beta,26-diol, and as an unusual tricyclic sesquiterpene. The compounds have been assayed for their phytotoxicity on lettuce at the concentrations ranging between 10(-4) and 10(-7)M. The activities of some compounds were similar to that of the herbicide pendimethalin.

  5. Mechanochemically synthesized cobalt monoselenide: structural characterization and optical properties

    NASA Astrophysics Data System (ADS)

    Achimovičová, Marcela; Daneu, Nina; Dutková, Erika; Zorkovská, Anna

    2017-03-01

    Chalcogenide semiconductor cobalt monoselenide, CoSe, was prepared from metallic cobalt and selenium powders in stoichiometric ratio by simple and fast mechanochemical synthesis after 120 min of milling in a planetary ball mill Pulverisette 6 (Fritsch, Germany) in an argon atmosphere. Crystal structure and morphology of the product were characterized by X-ray diffraction, specific surface area measurements, and transmission electron microscopy. X-ray diffraction analysis confirmed the hexagonal crystal structure of the product-CoSe (freboldite) with the average size of the crystallites 26 nm. Transmission electron microscopy analysis has revealed that CoSe nanostructures are composed of agglomerated and randomly oriented nanoparticles. The optical properties were studied using UV-Vis and photoluminescence spectroscopy. Mechanochemically synthesized CoSe nanostructures showed higher absorption in whole UV-Vis optical region and the determined band-gap energy 1.70 eV is blue-shifted relative to the bulk CoSe. Both UV-Vis and photoluminescence spectra indicate quantum size effect of CoSe nanocrystals.

  6. Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure.

    PubMed

    Can, Mehmet; Krucinska, Jolanta; Zoppellaro, Giorgio; Andersen, Niels H; Wedekind, Joseph E; Hersleth, Hans-Petter; Andersson, K Kristoffer; Bren, Kara L

    2013-09-23

    Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.

  7. Detailed Relationship Between Local Structure Polarons and Magnetization for La1-xCaxMnO3 (0.21 lt x lt 0.45)

    SciTech Connect

    F Bridges; L Downward; J Neumeier; T Tyson

    2011-12-31

    We present detailed local structure measurements (using the extended x-ray absorption fine structure technique) for the colossal magnetoresistive material La{sub 1-x}Ca{sub x}MnO{sub 3} (0.21 < x < 0.45) as a function of temperature and magnetic field. The local distortions of the Mn-O bonds are parameterized using {sigma}, the width of the Mn-O pair-distribution function (PDF). After subtracting thermal phonon contributions, we show that the contributions to {sigma}{sup 2} from polaron and Jahn-Teller (JT) distortions, {sigma}{sub JT/polaron}{sup 2}, are a universal function of the magnetization, independent of how the magnetization is achieved via changes in temperature or magnetic field. However this universal behavior is only observed for B fields {ge} 2 T, likely as a result of domain canting in low B fields. The resulting curve is well described by two straight lines with significantly different slopes. These regimes represent two distinctly differ distortions of the oxygen octahedra about the Mn. For low magnetizations up to {approx}65% of the theoretical maximum magnetization, M{sub T}, the slope is low and the distortion removed as the sample becomes magnetized is small - we argue this arises from polarons which have a low distortion around two (or possibly three) Mn sites. At high magnetizations large distortions per Mn site are removed as these sites become magnetized. The data are also analyzed in terms of a two Mn-O peak distribution using experimental standards for Mn-O. The results agree well with recent neutron PDF results but not with some earlier results. We discuss the limitations of assuming a two peak distribution in view of the two distortions needed to describe the Mn-O distortions as a function of T and B for B {ge} 2 T. It is likely that there is a distribution of longer bonds. Finally we show that with increasing B field, the Mn-Mn peak also has a small B-field-induced change - a measure at the unit cell level of magnetostriction but find

  8. Characterization of Polyimide Foams for Ultra-Lightweight Space Structures

    NASA Technical Reports Server (NTRS)

    Meador, Michael (Technical Monitor); Hillman, Keithan; Veazie, David R.

    2003-01-01

    Ultra-lightweight materials have played a significant role in nearly every area of human activity ranging from magnetic tapes and artificial organs to atmospheric balloons and space inflatables. The application range of ultra-lightweight materials in past decades has expanded dramatically due to their unsurpassed efficiency in terms of low weight and high compliance properties. A new generation of ultra-lightweight materials involving advanced polymeric materials, such as TEEK (TM) polyimide foams, is beginning to emerge to produce novel performance from ultra-lightweight systems for space applications. As a result, they require that special conditions be fulfilled to ensure adequate structural performance, shape retention, and thermal stability. It is therefore important and essential to develop methodologies for predicting the complex properties of ultra-lightweight foams. To support NASA programs such as the Reusable Launch Vehicle (RLV), Clark Atlanta University, along with SORDAL, Inc., has initiated projects for commercial process development of polyimide foams for the proposed cryogenic tank integrated structure (see figure 1). Fabrication and characterization of high temperature, advanced aerospace-grade polyimide foams and filled foam sandwich composites for specified lifetimes in NASA space applications, as well as quantifying the lifetime of components, are immensely attractive goals. In order to improve the development, durability, safety, and life cycle performance of ultra-lightweight polymeric foams, test methods for the properties are constant concerns in terms of timeliness, reliability, and cost. A major challenge is to identify the mechanisms of failures (i.e., core failure, interfacial debonding, and crack development) that are reflected in the measured properties. The long-term goal of the this research is to develop the tools and capabilities necessary to successfully engineer ultra-lightweight polymeric foams. The desire is to reduce density

  9. Structural characterization of the DC-SIGN-Lewis(X) complex.

    PubMed

    Pederson, Kari; Mitchell, Daniel A; Prestegard, James H

    2014-09-09

    Dendritic cell-specific intracellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) is a C-type lectin highly expressed on the surface of antigen-presenting dendritic cells. DC-SIGN mediates interactions among dendritic cells, pathogens, and a variety of epithelia, myeloid cells, and endothelia by binding to high mannose residues on pathogenic invaders or fucosylated residues on the membranes of other immune cells. Although these interactions are normally beneficial, they can also contribute to disease. The structural characterization of binding geometries is therefore of interest as a basis for the construction of mimetics that can mediate the effects of abnormal immune response. Here, we report the structural characteristics of the interaction of the DC-SIGN carbohydrate recognition domain (CRD) with a common fucosylated entity, the Lewis(X) trisaccharide (Le(X)), using NMR methods. Titration of the monomeric DC-SIGN CRD with Le(X) monitored by 2D NMR revealed significant perturbations of DC-SIGN cross-peak positions in (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra and identified residues near the binding site. Additionally, saturation transfer difference (STD) and transferred nuclear Overhauser effect (trNOE) NMR experiments, using a tetrameric form of DC-SIGN, identified binding epitopes and bound conformations of the Le(X) ligand. The restraints derived from these multiple experiments were used to generate models for the binding of Le(X) to the DC-SIGN CRD. Ranking of the models based on the fit of model-based simulations of the trNOE data and STD buildup curves suggested conformations distinct from those seen in previous crystal structures. The new conformations offer insight into how differences between binding of Lewis(X) and mannose-terminated saccharides may be propagated.

  10. Biochemical and structural characterization of Plasmodium falciparum glutamate dehydrogenase 2.

    PubMed

    Zocher, Kathleen; Fritz-Wolf, Karin; Kehr, Sebastian; Fischer, Marina; Rahlfs, Stefan; Becker, Katja

    2012-05-01

    Glutamate dehydrogenases (GDHs) play key roles in cellular redox, amino acid, and energy metabolism, thus representing potential targets for pharmacological interventions. Here we studied the functional network provided by the three known glutamate dehydrogenases of the malaria parasite Plasmodium falciparum. The recombinant production of the previously described PfGDH1 as hexahistidyl-tagged proteins was optimized. Additionally, PfGDH2 was cloned, recombinantly produced, and characterized. Like PfGDH1, PfGDH2 is an NADP(H)-dependent enzyme with a specific activity comparable to PfGDH1 but with slightly higher K(m) values for its substrates. The three-dimensional structure of hexameric PfGDH2 was solved to 3.1 Å resolution. The overall structure shows high similarity with PfGDH1 but with significant differences occurring at the subunit interface. As in mammalian GDH1, in PfGDH2 the subunit-subunit interactions are mainly assisted by hydrogen bonds and hydrophobic interactions, whereas in PfGDH1 these contacts are mediated by networks of salt bridges and hydrogen bonds. In accordance with this, the known bovine GDH inhibitors hexachlorophene, GW5074, and bithionol were more effective on PfGDH2 than on PfGDH1. Subcellular localization was determined for all three plasmodial GDHs by fusion with the green fluorescent protein. Based on our data, PfGDH1 and PfGDH3 are cytosolic proteins whereas PfGDH2 clearly localizes to the apicoplast, a plastid-like organelle specific for apicomplexan parasites. This study provides new insights into the structure and function of GDH isoenzymes of P. falciparum, which represent potential targets for the development of novel antimalarial drugs.

  11. Detailed Characterization of a Nanosecond-Lived Excited State: X-ray and Theoretical Investigation of the Quintet State in Photoexcited [Fe(terpy) 2 ] 2+

    DOE PAGES

    Vanko, Gyorgy; Bordage, Amelie; Papai, Matyas; ...

    2015-03-19

    Theoretical predictions show that depending on the populations of the Fe 3dxy, 3dxz, and 3dyz orbitals two possible quintet states can exist for the high-spin state of the photoswitchable model system [Fe(terpy)2]2+. The differences in the structure and molecular properties of these 5B2 and 5E quintets are very small and pose a substantial challenge for experiments to resolve them. Yet for a better understanding of the physics of this system, which can lead to the design of novel molecules with enhanced photoswitching performance, it is vital to determine which high-spin state is reached in the transitions that follow the lightmore » excitation. The quintet state can be prepared with a short laser pulse and can be studied with cutting-edge time-resolved X-ray techniques. Here we report on the application of an extended set of X-ray spectroscopy and scattering techniques applied to investigate the quintet state of [Fe(terpy)2]2+ 80 ps after light excitation. High-quality X-ray absorption, nonresonant emission, and resonant emission spectra as well as X-ray diffuse scattering data clearly reflect the formation of the high-spin state of the [Fe(terpy)2]2+ molecule; moreover, extended X-ray absorption fine structure spectroscopy resolves the Fe–ligand bond-length variations with unprecedented bond-length accuracy in time-resolved experiments. With ab initio calculations we determine why, in contrast to most related systems, one configurational mode is insufficient for the description of the low-spin (LS)–high-spin (HS) transition. We identify the electronic structure origin of the differences between the two possible quintet modes, and finally, we unambiguously identify the formed quintet state as 5E, in agreement with our theoretical expectations.« less

  12. 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

  13. Systematic assessment of coordinated activity cliffs formed by kinase inhibitors and detailed characterization of activity cliff clusters and associated SAR information.

    PubMed

    Dimova, Dilyana; Stumpfe, Dagmar; Bajorath, Jürgen

    2015-01-27

    From currently available kinase inhibitors and their activity data, clusters of coordinated activity cliffs were systematically derived and subjected to cluster index and index map analysis. Type I-like inhibitors with well-defined IC50 measurements were found to provide a large knowledge base of activity cliff clusters for 266 targets from nine kinase groups. On the basis of index map analysis, these clusters were systematically organized according to structural similarity of inhibitors and activity cliff diversity and prioritized for structure-activity relationship (SAR) analysis. From prioritized clusters, interpretable SAR information can be extracted. It is also shown that activity cliff clusters formed by ATP site-directed inhibitors often represent local SAR environments of rather different complexity and interpretability. In addition, activity cliff clusters including promiscuous kinase inhibitors have been determined. Only a small subset of inhibitors was found to change activity cliff roles in different clusters. The activity cliff clusters described herein and their index map organization substantially enrich SAR information associated with kinase inhibitors in compound subsets of limited size. The cluster and index map information is made available upon request to provide opportunities for further SAR exploration. On the basis of our analysis and the data provided, activity cliff clusters and corresponding inhibitor series for kinase targets of interest can be readily selected.

  14. Crowdsourcing detailed flood data

    NASA Astrophysics Data System (ADS)

    Walliman, Nicholas; Ogden, Ray; Amouzad*, Shahrzhad

    2015-04-01

    Over the last decade the average annual loss across the European Union due to flooding has been 4.5bn Euros, but increasingly intense rainfall, as well as population growth, urbanisation and the rising costs of asset replacements, may see this rise to 23bn Euros a year by 2050. Equally disturbing are the profound social costs to individuals, families and communities which in addition to loss of lives include: loss of livelihoods, decreased purchasing and production power, relocation and migration, adverse psychosocial effects, and hindrance of economic growth and development. Flood prediction, management and defence strategies rely on the availability of accurate information and flood modelling. Whilst automated data gathering (by measurement and satellite) of the extent of flooding is already advanced it is least reliable in urban and physically complex geographies where often the need for precise estimation is most acute. Crowdsourced data of actual flood events is a potentially critical component of this allowing improved accuracy in situations and identifying the effects of local landscape and topography where the height of a simple kerb, or discontinuity in a boundary wall can have profound importance. Mobile 'App' based data acquisition using crowdsourcing in critical areas can combine camera records with GPS positional data and time, as well as descriptive data relating to the event. This will automatically produce a dataset, managed in ArcView GIS, with the potential for follow up calls to get more information through structured scripts for each strand. Through this local residents can provide highly detailed information that can be reflected in sophisticated flood protection models and be core to framing urban resilience strategies and optimising the effectiveness of investment. This paper will describe this pioneering approach that will develop flood event data in support of systems that will advance existing approaches such as developed in the in the UK

  15. Structural Characterization of the Fla2 Flagellum of Rhodobacter sphaeroides

    PubMed Central

    de la Mora, Javier; Uchida, Kaoru; del Campo, Ana Martínez; Camarena, Laura; Aizawa, Shin-Ichi

    2015-01-01

    ABSTRACT Rhodobacter sphaeroides is a free-living alphaproteobacterium that contains two clusters of functional flagellar genes in its genome: one acquired by horizontal gene transfer (fla1) and one that is endogenous (fla2). We have shown that the Fla2 system is normally quiescent and under certain conditions produces polar flagella, while the Fla1 system is always active and produces a single flagellum at a nonpolar position. In this work we purified and characterized the structure and analyzed the composition of the Fla2 flagellum. The number of polar filaments per cell is 4.6 on average. By comparison with the Fla1 flagellum, the prominent features of the ultra structure of the Fla2 HBB are the absence of an H ring, thick and long hooks, and a smoother zone at the hook-filament junction. The Fla2 helical filaments have a pitch of 2.64 μm and a diameter of 1.4 μm, which are smaller than those of the Fla1 filaments. Fla2 filaments undergo polymorphic transitions in vitro and showed two polymorphs: curly (right-handed) and coiled. However, in vivo in free-swimming cells, we observed only a bundle of filaments, which should probably be left-handed. Together, our results indicate that Fla2 cell produces multiple right-handed polar flagella, which are not conventional but exceptional. IMPORTANCE R. sphaeroides possesses two functional sets of flagellar genes. The fla1 genes are normally expressed in the laboratory and were acquired by horizontal transfer. The fla2 genes are endogenous and are expressed in a Fla1− mutant grown phototrophically and in the absence of organic acids. The Fla1 system produces a single lateral or subpolar flagellum, and the Fla2 system produces multiple polar flagella. The two kinds of flagella are never expressed simultaneously, and both are used for swimming in liquid media. The two sets of genes are certainly ready for responding to specific environmental conditions. The characterization of the Fla2 system will help us to understand

  16. Structural Characterization of the Ag/ybco Interface

    NASA Astrophysics Data System (ADS)

    Tidjani, Mohammed Elkhamis

    1990-01-01

    The present research is intended to characterize the interface microstructure and long term stability of the deposited silver metal in contact to the superconducting oxide YBa_2Cu_3O _{rm 7-x} (YBCO). High resolution transmission electron microscopy (HRTEM) observations of the interfacial regions reveal that Ag contacts to YBCO occurred without any intermediate phase formation at the interface. The Ag metal exhibits a preferred orientation relationship with YBCO, in which the densely packed planes and directions of the metal are parallel to those of the superconductor. The formation of (111) interfaces and facets during deposition indicates that these planes are associated with the lowest interfacial energy. The as-deposited Ag film exhibits a granular morphology, and the Ag grains are often twinned along the (111) plane while the surface of YBCO is mostly rough and structurally unstable. Annealing of the Ag/YBCO interface resulted in outdiffusion of yttrium and oxygen at regions where the surface of YBCO was rough. This diffusion, however, did not result in the formation of continuous layers at the Ag/YBCO interface but only to growth of Ag_2 Y and Ag_2O inclusions. Thus it is believed that the stability of the Ag/YBCO depends on the quality of the surface of YBCO, especially its structure. Treatment of the surface of YBCO by ion-bombardment yielded flat surfaces but damaged a layer of about 30A. Such a cleaning process improved the quality of the deposited Ag since the Ag grains were larger and contained low defects concentration. The same orientation relationships between Ag and YBCO were observed after cleaning the surface of YBCO which implied that the destruction of the structure at the surface is only partial. Deposition of Ag in the same chamber where YBCO was initially grown, to minimize the contamination of the surface of YBCO, also was not effective in enhancing the structure of the Ag/YBCO interface. The roughness of the surface of YBCO did not decrease

  17. Characterization of structural relaxation in inorganic glasses using length dilatometry

    NASA Astrophysics Data System (ADS)

    Koontz, Erick

    The processes that govern how a glass relaxes towards its thermodynamic quasi-equilibrium state are major factors in understanding glass behavior near the glass transition region, as characterized by the glass transition temperature (Tg). Intrinsic glass properties such as specific volume, enthalpy, entropy, density, etc. are used to map the behavior of the glass network below in and near the transition region. The question of whether a true thermodynamic second order phase transition takes place in the glass transition region is another pending question. Linking viscosity behavior to entropy, or viewing the glass configuration as an energy landscape are just a couple of the most prevalent methods used for attempting to understand the glass transition. The structural relaxation behavior of inorganic glasses is important for more than scientific reasons, many commercial glass processing operations including glass melting and certain forms of optical fabrication include significant time spent in the glass transition region. For this reason knowledge of structural relaxation processes can, at a minimum, provide information for annealing duration of melt-quenched glasses. The development of a predictive model for annealing time prescription has the potential to save glass manufacturers significant time and money as well as increasing volume throughput. In optical hot forming processes such as precision glass molding, molded optical components can significantly change in shape upon cooling through the glass transition. This change in shape is not scientifically predictable as of yet though manufacturers typically use empirical rules developed in house. The classification of glass behavior in the glass transition region would allow molds to be accurately designed and save money for the producers. The work discussed in this dissertation is comprised of the development of a dilatometric measurement and characterization method of structural relaxation. The measurement and

  18. Horizontal Cross Bracing Detail, Vertical Cross Bracing Detail, Horizontal Cross ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Horizontal Cross Bracing Detail, Vertical Cross Bracing Detail, Horizontal Cross Bracing Detail, Vertical Cross Bracing-End Detail - Cumberland Covered Bridge, Spanning Mississinewa River, Matthews, Grant County, IN

  19. Characterization of structural and electronic properties of nanoscale semiconductor device structures using cross-sectional scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Rosenthal, Paul Arthur

    Scanning probe microscopy (SPM) offers numerous advantages over metrology tools traditionally used for semiconductor materials and device characterization including high lateral spatial resolution, and relative ease of use. Cross-sectional SPM allows material and device measurements including layer thickness metrology and p-n junction delineation on actual nanoscale device structures. Site-specific SPM allows measurements to be performed on modern devices with real, non-arbitrary geometries including deep-submicron Si device structures. In Chapter II we present theoretical analysis and experimental results of capacitive force microscopy studies of AlxGa1-xAs/GaAs heterojunction bipolar transistor structures. The contrast obtained yields clear delineation of individual device layers based on doping, and enables a precise determination of the difference in basewidth between the two HBT samples examined. We experimentally determine a charged surface state density on the GaAs {110} surface that is consistent with published values. In Chapter III we present cross-sectional scanning capacitance microscopy (SCM) of nanoscale group IV Si device structures. Sample preparation techniques are discussed in context with recent experimental results from the literature. We then presented a theoretical calculation of the flat-band and threshold voltage of Si-MOSFETs as a function of doping including error analysis due to oxide thickness variations. Application to nanoscale FIB implanted Si is presented. The SCM contrast evolves as a function of applied bias as expected based on theoretical modeling of the tip-sample system as an MOS-capacitor. In Chapter IV we apply cross-sectional SCM to directly measure the electronic properties of a 120 nm gate length p-MOSFET including super-halo implants. Bias-dependent SCM images allow us to delineate the individual device regions and image the n+ super-halo implants. We have demonstrated the specific SCM bias conditions necessary for

  20. Dynamic quasistatic characterization of finite elements for shell structures.

    SciTech Connect

    Thomas, Jesse David

    2010-11-01

    Finite elements for shell structures have been investigated extensively, with numerous formulations offered in the literature. These elements are vital in modern computational solid mechanics due to their computational efficiency and accuracy for thin and moderately thick shell structures, allowing larger and more comprehensive (e.g. multi-scale and multi-physics) simulations. Problems now of interest in the research and development community are routinely pushing our computational capabilities, and thus shell finite elements are being used to deliver efficient yet high quality computations. Much work in the literature is devoted to the formulation of shell elements and their numerical accuracy, but there is little published work on the computational characterization and comparison of shell elements for modern solid mechanics problems. The present study is a comparison of three disparate shell element formulations in the Sandia National Laboratories massively parallel Sierra Solid Mechanics code. A constant membrane and bending stress shell element (Key and Hoff, 1995), a thick shell hex element (Key et al., 2004) and a 7-parameter shell element (Buechter et al., 1994) are available in Sierra Solid Mechanics for explicit transient dynamic, implicit transient dynamic and quasistatic calculations. Herein these three elements are applied to a set of canonical dynamic and quasistatic problems, and their numerical accuracy, computational efficiency and scalability are investigated. The results show the trade-off between the relative inefficiency and improved accuracy of the latter two high quality element types when compared with the highly optimized and more widely used constant membrane and bending stress shell element.

  1. Structural characterization of the lignin from jute (Corchorus capsularis) fibers.

    PubMed

    del Río, José C; Rencoret, Jorge; Marques, Gisela; Li, Jiebing; Gellerstedt, Göran; Jiménez-Barbero, Jesús; Martínez, Angel T; Gutiérrez, Ana

    2009-11-11

    The structural characteristics of the lignin from jute (Corchorus capsularis ) fibers, which are used for high-quality paper pulp production, were studied. The lignin content (13.3% Klason lignin) was high compared to other nonwoody bast fibers used for pulp production. The lignin structure was characterized by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), 2D-NMR, and thioacidolysis. Upon Py-GC/MS, jute fibers released predominantly products from syringylpropanoid units with the S/G ratio being 2.1 and a H/G/S composition of 2:33:65. 2D-NMR of the milled wood lignin (MWL) isolated from jute fibers showed a predominance of beta-O-4' aryl ether linkages (72% of total side chains), followed by beta-beta' resinol-type linkages (16% of total side chains) and lower amounts of beta-5' phenylcoumaran (4%) and beta-1' spirodienone-type (4%) linkages and cinnamyl end groups (4%). The high predominance of the S-lignin units, together with the high proportion of beta-O-4' aryl ether linkages, which are easily cleaved during alkaline cooking, are advantageous for pulping. On the other hand, a small percentage (ca. 4%) of the lignin side chain was found to be acetylated at the gamma-carbon, predominantly over syringyl units. The analysis of desulphurated thioacidolysis dimers provided additional information on the relative abundances of the various carbon-carbon and diaryl ether bonds and the type of units (syringyl or guaiacyl) involved in each of the above linkage types. Interestingly, the major part of the beta-beta' dimers included two syringyl units, indicating that most of the beta-beta' substructures identified in the HSQC spectra were of the syringaresinol type (pinoresinol being absent), as already observed in the lignin of other angiosperms.

  2. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

    PubMed Central

    Machiela, Mitchell J.; Zhou, Weiyin; Sampson, Joshua N.; Dean, Michael C.; Jacobs, Kevin B.; Black, Amanda; Brinton, Louise A.; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S.; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M.; Gaudet, Mia M.; Haiman, Christopher A.; Hankinson, Susan E.; Hartge, Patricia; Henderson, Brian E.; Hong, Yun-Chul; Hosgood, H. Dean; Hsiung, Chao A.; Hu, Wei; Hunter, David J.; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Matsuo, Keitaro; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A.; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C.; Albanes, Demetrius; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Berndt, Sonja I.; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C.; Cook, Michael B.; Cullen, Michael; Davis, Faith G.; Ding, Ti; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Freedman, Neal D.; Fuchs, Charles S.; Gao, Yu-Tang; Gapstur, Susan M.; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Greene, Mark H.; Hallmans, Goran; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hoover, Robert N.; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M.; Malats, Nuria; McGlynn, Katherine A.; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G.; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M.; Savage, Sharon A.; Schwartz, Ann G.; Schwartz, Kendra L.; Sesso, Howard D.; Severi, Gianluca; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J.; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wu, Xifeng; Wunder, Jay S.; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G.; de Andrade, Mariza; Barnes, Kathleen C.; Beaty, Terri H.; Bierut, Laura J.; Desch, Karl C.; Doheny, Kimberly F.; Feenstra, Bjarke; Ginsburg, David; Heit, John A.; Kang, Jae H.; Laurie, Cecilia A.; Li, Jun Z.; Lowe, William L.; Marazita, Mary L.; Melbye, Mads; Mirel, Daniel B.; Murray, Jeffrey C.; Nelson, Sarah C.; Pasquale, Louis R.; Rice, Kenneth; Wiggs, Janey L.; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A.; Laurie, Cathy C.; Caporaso, Neil E.; Yeager, Meredith; Chanock, Stephen J.

    2015-01-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10−31) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  3. Structure and absolute configuration of ginkgolide B characterized by IR- and VCD spectroscopy.

    PubMed

    Andersen, Niels H; Christensen, Niels Johan; Lassen, Peter R; Freedman, Teresa B N; Nafie, Laurence A; Strømgaard, Kristian; Hemmingsen, Lars

    2010-02-01

    Experimental and calculated (B3LYP/6-31G(d)) vibrational circular dichroism (VCD) and IR spectra are compared, illustrating that the structure and absolute configuration of ginkgolide B (GB) may be characterized directly in solution. A conformational search for GB using MacroModel and subsequent DFT optimizations (B3LYP/6-31G(d)) provides a structure for the lowest energy conformer which agrees well with the structure determined by X-ray diffraction. In addition, a conformer at an energy of 7 kJ mol(-1) (B3LYP/6-311+G(2d,2p)) with respect to the lowest energy conformer is predicted, displaying different intramolecular hydrogen bonding. Differences between measured and calculated IR and VCD spectra for GB at certain wavenumbers are rationalized in terms of interactions with solvent, intermolecular GB-GB interactions, and the potential presence of more than one conformer. This is the first detailed investigation of the spectroscopic fingerprint region (850-1300 cm(-1)) of the natural product GB employing infrared absorption and VCD spectroscopy.

  4. Rockfall source characterization at high rock walls in complex geological settings by photogrammetry, structural analysis and DFN techniques

    NASA Astrophysics Data System (ADS)

    Agliardi, Federico; Riva, Federico; Galletti, Laura; Zanchi, Andrea; Crosta, Giovanni B.

    2016-04-01

    Rockfall quantitative risk analysis in areas impended by high, subvertical cliffs remains a challenge, due to the difficult definition of potential rockfall sources, event magnitude scenarios and related probabilities. For this reasons, rockfall analyses traditionally focus on modelling the runout component of rockfall processes, whereas rock-fall source identification, mapping and characterization (block size distribution and susceptibility) are over-simplified in most practical applications, especially when structurally complex rock masses are involved. We integrated field and remote survey and rock mass modelling techniques to characterize rock masses and detect rockfall source in complex geo-structural settings. We focused on a test site located at Valmadrera, near Lecco (Southern Alps, Italy), where cliffs up to 600 m high impend on a narrow strip of Lake Como shore. The massive carbonates forming the cliff (Dolomia Principale Fm), normally characterized by brittle structural associations due to their high strength and stiffness, are here involved in an ENE-trending, S-verging kilometre-scale syncline. Brittle mechanisms associated to folding strongly controlled the nature of discontinuities (bedding slip, strike-slip faults, tensile fractures) and their attributes (spacing and size), as well as the spatial variability of bedding attitude and fracture intensity, with individual block sizes up to 15 m3. We carried out a high-resolution terrestrial photogrammetric survey from distances ranging from 1500 m (11 camera stations from the opposite lake shore, 265 pictures) to 150 m (28 camera stations along N-S directed boat routes, 200 pictures), using RTK GNSS measurements for camera station geo-referencing. Data processing by Structure-from-Motion techniques resulted in detailed long-range (1500 m) and medium-range (150 to 800 m) point clouds covering the entire slope with maximum surface point densities exceeding 50 pts/m2. Point clouds allowed a detailed

  5. Structural Characterization of Hydroxyl Radical Adducts in Aqueous Media

    NASA Astrophysics Data System (ADS)

    Janik, Ireneusz; Tripathi, G. N. R.

    2015-06-01

    The oxidation by the hydroxyl (OH) radical is one of the most widely studied reactions because of its central role in chemistry, biology, organic synthesis, and photocatalysis in aqueous environments, wastewater treatment, and numerous other chemical processes. Although the redox potential of OH is very high, direct electron transfer (ET) is rarely observed. If it happens, it mostly proceeds through the formation of elusive OH adduct intermediate which facilitates ET and formation of hydroxide anion. Using time resolved resonance Raman technique we structurally characterized variety of OH adducts to sulfur containing organic compounds, halide ions as well as some metal cations. The bond between oxygen of OH radical and the atom of oxidized molecule differs depending on the nature of solute that OH radical reacts with. For most of sulfur containing organics, as well as halide and pseudo-halide ions, our observation suggested that this bond has two-center three-electron character. For several metal aqua ions studied, the nature of the bond depends on type of the cation being oxidized. Discussion on spectral parameters of all studied hydroxyl radical adducts as well as the role solvent plays in their stabilization will be presented.

  6. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  7. Structural Characterization of a Capillary Microfluidic Chip Using Microreflectance.

    PubMed

    Lastras-Martínez, Luis F; Balderas-Navarro, Raul E; Castro-García, Ricardo; Hernández-Vidales, Karen; Almendarez-Rodríguez, Juan; Herrera-Jasso, Rafael; Prinz, Adrian; Bergmair, Iris

    2016-10-18

    The structural characterization of capillary microfluidic chips is important for reliable applications. In particular, nondestructive diagnostic tools to assess geometrical dimensions and their correlations with control processes are of much importance, preferably if they are implemented in situ. Several techniques to accomplish this task have been reported; namely, optical coherence tomography (OCT) jointly with confocal fluorescence microscopy (CFM) to investigate internal features of lab-on-a-chip technologies. In this paper, we report on the use of a simple optical technique, based on near-normal incidence microreflectance, which allows mapping internal features of a microfluidic chip in a straightforward way. Our setup is based on a charge-coupled device camera that allows a lateral resolution of ∼2.5 µm and allows us to measure in the wavelength range of 640-750 nm. The technique takes advantage of the Fabry-Perot interferences features in the reflectance spectra, which are further analyzed by a discrete Fourier transform. In this way, the amplitude of the Fourier coefficients is modulated by the presence of a microfluidic channel.

  8. Characterization of a rice bran oil structured lipid.

    PubMed

    Jennings, Brenda H; Akoh, Casimir C

    2009-04-22

    Rice bran oil (RBO) was enzymatically modified in a continuous packed bed bioreactor to incorporate caprylic acid with Lipozyme RM IM as biocatalyst. The reaction product was purified by short-path distillation. Rice bran oil structured lipid (RBOSL) contained 32.1 mol % caprylic acid. Positional analysis revealed 0.7 mol % caprylic acid at the sn-2 position and 47.8 mol % caprylic acid at the sn-1,3 positions. Composition of free fatty acids and smoke point of RBO and RBOSL were not significantly different. Saponification value, iodine value, and viscosity of RBO were significantly different from those of RBOSL. The color of RBOSL was darker, more yellow and less green than RBO. Volatile compounds in RBO and RBOSL were determined by GC-MS. Melting onset temperatures of RBO and RBOSL were not significantly different, while melting end point temperatures and melting enthalpies were significantly different. This characterization study results will help determine potential food applications of RBOSL.

  9. Structure and Mixing Characterization of Variable Density Transverse Jet Flows

    NASA Astrophysics Data System (ADS)

    Gevorkyan, Levon

    (CVP) and the generation of strong upstream shear layer instability. In contrast, weak, convectively unstable upstream shear layers corresponded with asymmetries in the jet cross-sectional shape and/or lack of a CVP structure. While momentum flux ratio J and density ratio S most significantly determined the strength of the instabilities and CVP structures, an additional dependence on jet Reynolds number for CVP formation was found, with significant increases in jet Reynolds number resulting in enhanced symmetry and CVP generation. The mixing characteristics of Rej = 1900 jets of various J, S, and injector type were explored in detail in the present studies using jet centerplane and cross-sectional PLIF measurements. Various mixing metrics such as the jet fluid centerline concentration decay, Unmixedness, and Probability Density Function (PDF) were applied systematically using a novel method for comparing jets with different mass flux characteristics. It was found that when comparing mixing metrics along the jet trajectory, strengthening the upstream shear layer instability by reducing J, and achieving absolutely unstable conditions, enhanced overall mixing. Reducing density ratio S for larger J values, which under equidensity (S = 1.00) conditions would create a convectively unstable shear layer, was also observed to enhance mixing. On the other hand, reducing S for low J conditions, which are known to produce absolutely unstable upstream shear layers even for equidensity cases, was actually observed to reduce mixing, a result attributed to a reduction in crossfiow fluid entrainment into shear layer vortex cores as jet density was reduced. Comparing injectors, the flush-mounted pipe was generally the best mixer, whereas the worst mixer was the nozzle that was elevated above the crossfiow boundary layer due to upstream shear layer co-flow generated by the elevated nozzle contour; this co-flow was observed here and in prior studies to stabilize the shear layer. The

  10. Complete structural characterization of ceramides as [M-H](-) ions by multiple-stage linear ion trap mass spectrometry.

    PubMed

    Hsu, Fong-Fu

    2016-11-01

    Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MS(n)) towards complete structural determination of ceramides in ten major families characterized as the [M-H](-) ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS(2) spectrum, while the sequential MS(3) and MS(4) spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail.

  11. Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

    SciTech Connect

    Das, Sumanta; Stone, David; Convey, Diana; Neithalath, Narayanan

    2014-12-15

    The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.

  12. The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.

    PubMed Central

    Bode, W.; Turk, D.; Karshikov, A.

    1992-01-01

    Thrombin is a multifunctional serine proteinase that plays a key role in coagulation while exhibiting several other key cellular bioregulatory functions. The X-ray crystal structure of human alpha-thrombin was determined in its complex with the specific thrombin inhibitor D-Phe-Pro-Arg chloromethylketone (PPACK) using Patterson search methods and a search model derived from trypsinlike proteinases of known spatial structure (Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R., & Hofsteenge, J., 1989, EMBO J. 8, 3467-3475). The crystallographic refinement of the PPACK-thrombin model has now been completed at an R value of 0.156 (8 to 1.92 A); in particular, the amino- and the carboxy-termini of the thrombin A-chain are now defined and all side-chain atoms localized; only proline 37 was found to be in a cis-peptidyl conformation. The thrombin B-chain exhibits the characteristic polypeptide fold of trypsinlike serine proteinases; 195 residues occupy topologically equivalent positions with residues in bovine trypsin and 190 with those in bovine chymotrypsin with a root-mean-square (r.m.s.) deviation of 0.8 A for their alpha-carbon atoms. Most of the inserted residues constitute novel surface loops. A chymotrypsinogen numbering is suggested for thrombin based on the topological equivalences. The thrombin A-chain is arranged in a boomeranglike shape against the B-chain globule opposite to the active site; it resembles somewhat the propeptide of chymotrypsin(ogen) and is similarly not involved in substrate and inhibitor binding. Thrombin possesses an exceptionally large proportion of charged residues. The negatively and positively charged residues are not distributed uniformly over the whole molecule, but are clustered to form a sandwichlike electrostatic potential; in particular, two extended patches of mainly positively charged residues occur close to the carboxy-terminal B-chain helix (forming the presumed heparin-binding site) and on the surface of loop segment 70

  13. Structural characterization and electronic structure of laser treated TiN thin film

    SciTech Connect

    Soni, Sheetal; Nair, K. G. M.; Phase, D. M.; Gupta, Ratnesh

    2012-06-05

    TiN thin films prepared by laser treatment using Kr-F excimer laser in the controlled atmosphere. The depth distribution and composition of nitrogen and contaminated oxygen have been determined by non-Rutherford proton backscattering using 1.7 MeV Tendetron accelerator. The electronic structure of TiN thin film have been characterized by resonant photoelectron spectroscopy using indus-I synchrotron radiation. Specifically, complex resonance profile that shows the enhancement at 45 eV which is consistent with the resonant photoemission of Ti 3d states involved in the Titanium nitride and oxide.

  14. Structural characterization and electronic structure of laser treated TiN thin film

    NASA Astrophysics Data System (ADS)

    Soni, Sheetal; Nair, K. G. M.; Phase, D. M.; Gupta, Ratnesh

    2012-06-01

    TiN thin films prepared by laser treatment using Kr-F excimer laser in the controlled atmosphere. The depth distribution and composition of nitrogen and contaminated oxygen have been determined by non-Rutherford proton backscattering using 1.7 MeV Tendetron accelerator. The electronic structure of TiN thin film have been characterized by resonant photoelectron spectroscopy using indus-I synchrotron radiation. Specifically, complex resonance profile that shows the enhancement at 45 eV which is consistent with the resonant photoemission of Ti 3d states involved in the Titanium nitride and oxide.

  15. The Evaluation of Complex Borehole Geophysics and Corescanning: for Detailed Characterization of Oriented Fracture Sets, Zones, and Hydraulic Flow on Different Scales. A Case Study: Moragy Granite, Mecsek Mts., Hungary

    NASA Astrophysics Data System (ADS)

    Maros, G.; Zilahi-Sebess, L.; Dudko, A.; Koroknai, Z.

    2005-12-01

    Our presentation outlines the methodology to determine the relationship between fractures and flow systems, and it tries to homogenize the results deriving from methods of different resolutions in a geological model. The granite suffered multi-phase brittle deformation during the Alpine orogene, the fractures renewed several times and were filled with multi-generation infillings. The cores were scanned with the ImaGeo system, the fractures were oriented, characterized in detail from geological and geophysical point of views, and structurally evaluated. A structural model was sketched (Maros et al 2004). The results were refined by the information received from geophysical data, primarily from well-logging (Zilahi-Sebess et al 2003), but radar measurements, crosshole velocity tomography were also used (Toros et al 2004). Transmissivity in granite: 10-6-10-12, main fractures: 10-6-10-5 m2/s. Porous and fracture flow models were set up (Benedek et al 2003, Balla et al 2004). Correlations were found between the core-logging and the well-logging: acoustic openness, density, acoustic velocity, resistivity versus fracture frequency, fracture zones versus HPF influx places. The complex evaluation made the determination of the size and dip of fracture zones more precise. The flow characteristics of individual fractures and fracture zones, however, are influenced by their unique features; no parameter-group can be selected that definitely produces permeable or impermeable fractures. The interpretation of the observations carried out on different scales can be done in several ways. One method is to use methods of different resolutions densely enough to be representative. We examined the relation of information deriving from high resolution methods and the well-logging. On the basis of the depth-trends it is possible to extrapolate the information around the borehole. The relationship with the geophysical surveys is possible through the resistivity and acoustic measurements

  16. Underground structure characterization using motor vehicles as passive seismic sources

    NASA Astrophysics Data System (ADS)

    Kuzma, H. A.; Liu, Y.; Zhao, Y.; Rector, J.; Vaidya, S.

    2009-12-01

    The ability to detect and characterize underground voids will be critical to the success of On-Site Inspections (OSI) as mandated by the nuclear Comprehensive Test Ban Treaty (CTBT). OSIs may be conducted in order to successfully locate the Ground Zero of underground tests as well as infrastructure related to testing. Recently, our team has shown the potential of a new technique to detect underground objects using the amplitude of seismic surface waves generated by motor vehicles. In an experiment conducted in June, 2009 we were able to detect an abandoned railroad tunnel by recognizing a clear pattern in the surface waves scattered by the tunnel, using a signal generated by driving a car on a dirt road across the tunnel. Synthetic experiments conducted using physically realistic wave-equation models further suggest that the technique can be readily applied to detecting underground features: it may be possible to image structures of importance to OSI simply by laying out an array of geophones (or using an array already in place for passive listening for event aftershocks) and driving vehicles around the site. We present evidence from a set of field experiments and from synthetic modeling and inversion studies to illustrate adaptations of the technique for OSI. Signature of an abandoned underground railroad tunnel at Donner Summit, CA. To produce this image, a line of geophones was placed along a dirt road perpendicular to the tunnel (black box) and a single car was driven along the road. A normalized mean power-spectrum is displayed on a log scale as a function of meters from the center of the tunnel. The top of the tunnel was 18m below ground surface. The tunnel anomaly is made up of a shadow (light) directly above the tunnel and amplitude build-up (dark) on either side of the tunnel. The size of the anomaly (6 orders of magnitude) suggests that the method can be extended to find deep structures at greater distances from the source and receivers.

  17. Detailed Geological Modelling in Urban Areas focused on Structures relevant to the Near Surface Groundwater Flow in the context of Climatic Changes

    NASA Astrophysics Data System (ADS)

    Bach, T.; Pallesen, T. M.; Jensen, N. P.; Mielby, S.; Sandersen, P.; Kristensen, M.

    2015-12-01

    This case demonstrates a practical example from the city of Odense (DK) where new geological modeling techniques has been developed and used in the software GeoScene3D, to create a detailed voxel model of the anthropogenic layer. The voxel model has been combined with a regional hydrostratigraphic layer model. The case is part of a pilot project partly financed by VTU (Foundation for Development of Technology in the Danish Water Sector) and involves many different datatypes such as borehole information, geophysical data, human related elements (landfill, pipelines, basements, roadbeds etc). In the last few years, there has been increased focus on detailed geological modeling in urban areas. The models serve as important input to hydrological models. This focus is partly due to climate changes as high intensity rainfalls are seen more often than in the past, and water recharge is a topic too. In urban areas, this arises new challenges. There is a need of a high level of detailed geological knowledge for the uppermost zone of the soil, which typically are problematic due to practically limitations, especially when using geological layer models. Furthermore, to accommodate the need of a high detail, all relevant available data has to be used in the modeling process. Human activity has deeply changed the soil layers, e.g. by constructions as roadbeds, buildings with basements, pipelines, landfill etc. These elements can act as barriers or pathways regarding surface near groundwater flow and can attribute to local flooding or mobilization and transport of contaminants etc. A geological voxel model is built by small boxes (a voxel). Each box can contain several parameters, ex. lithology, transmissivity or contaminant concentration. Human related elements can be implemented using tools, which gives the modeler advanced options for making detailed small-scale models. This case demonstrates the workflow and the resulting geological model for the pilot area.

  18. Structural and functional characterization of Delphinus delphis hemoglobin system.

    PubMed

    Manconi, Barbara; Messana, Irene; Maggiani, Federica; Olianas, Alessandra; Pellegrini, Mariagiuseppina; Crnjar, Roberto; Castagnola, Massimo; Giardina, Bruno; Sanna, Maria Teresa

    2009-11-01

    Structural analysis of the hemoglobin (Hb) system of Delphinus delphis revealed a high globin multiplicity: HPLC-electrospray ionization-mass spectrometry (ESI-MS) analysis evidenced three major beta (beta1 16,022 Da, beta2 16,036 Da, beta3 16,036 Da, labeled according to their progressive elution times) and two major alpha globins (alpha1 15,345 Da, alpha2 15,329 Da). ESI-tandem mass and nucleotide sequence analyses showed that beta2 globin differs from beta1 for the substitution Val126 --> Leu, while beta3 globin differs from beta2 for the isobaric substitution Lys65 --> Gln. The alpha2 globin differs from the alpha1 for the substitution Ser15 --> Ala. Anion-exchange chromatography allowed the separation of two Hb fractions and HPLC-ESI-MS analysis revealed that the fraction with higher pI (HbI) contained beta1, beta2 and both the alpha globins, and the fraction with lower pI (HbII) contained beta3 and both the alpha globins. Both D. delphis Hb fractions displayed a lower intrinsic oxygen affinity, a decreased effect of 2,3-BPG and a reduced cooperativity with respect to human HbA(0), with HbII showing the more pronounced differences. With respect to HbA(0), either the substitution Probeta5 --> Gly or the Probeta5 --> Ala is present in all the cetacean beta globins sequenced so far, and it has been hypothesized that position 5 of beta globins may have a role in the interaction with 2,3-BPG. Regarding the particularly lowered cooperativity of HbII, it is interesting to observe that the variant human HbA, characterized by the substitution Lysbeta65 --> Gln (HbJ-Cairo) has a decreased cooperativity with respect to HbA(0).

  19. Structural characterization of toxic oligomers that are kinetically trapped during α-synuclein fibril formation

    PubMed Central

    Chen, Serene W.; Drakulic, Srdja; Deas, Emma; Ouberai, Myriam; Aprile, Francesco A.; Arranz, Rocío; Ness, Samuel; Roodveldt, Cintia; Guilliams, Tim; De-Genst, Erwin J.; Klenerman, David; Wood, Nicholas W.; Knowles, Tuomas P.J.; Alfonso, Carlos; Rivas, Germán; Abramov, Andrey Y.; Valpuesta, José María; Dobson, Christopher M.; Cremades, Nunilo

    2015-01-01

    We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species. PMID:25855634

  20. Structural characterization of toxic oligomers that are kinetically trapped during α-synuclein fibril formation.

    PubMed

    Chen, Serene W; Drakulic, Srdja; Deas, Emma; Ouberai, Myriam; Aprile, Francesco A; Arranz, Rocío; Ness, Samuel; Roodveldt, Cintia; Guilliams, Tim; De-Genst, Erwin J; Klenerman, David; Wood, Nicholas W; Knowles, Tuomas P J; Alfonso, Carlos; Rivas, Germán; Abramov, Andrey Y; Valpuesta, José María; Dobson, Christopher M; Cremades, Nunilo

    2015-04-21

    We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species.

  1. Nanoscale structural and electronic characterization of α-RuCl3 layered compound

    NASA Astrophysics Data System (ADS)

    Ziatdinov, Maxim; Maksov, Artem; Banerjee, Arnab; Zhou, Wu; Berlijn, Tom; Yan, Jiaqiang; Nagler, Stephen; Mandrus, David; Baddorf, Arthur; Kalinin, Sergei

    The exceptional interplay of spin-orbit effects, Coulomb interaction, and electron-lattice coupling is expected to produce an elaborate phase space of α-RuCl3 layered compound, which to date remains largely unexplored. Here we employ a combination of scanning transmission electron microscopy (STEM) and scanning tunneling microscopy (STM) for detailed evaluation of the system's microscopic structural and electronic orders with a sub-nanometer precision. The STM and STEM measurements are further supported by neutron scattering, X-Ray diffraction, density functional theory (DFT), and multivariate statistical analysis. Our results show a trigonal distortion of Cl octahedral ligand cage along the C3 symmetry axes in each RuCl3 layer. The lattice distortion is limited mainly to the Cl subsystem leaving the Ru honeycomb lattice nearly intact. The STM topographic and spectroscopic characterization reveals an intra unit cell electronic symmetry breaking in a spin-orbit coupled Mott insulating phase on the Cl-terminated surface of α-RuCl3. The associated long-range charge order (CO) pattern is linked to a surface component of Cl cage distortion. We finally discuss a fine structure of CO and its potential relation to variations of average unit cell geometries found in multivariate analysis of STEM data. The research was sponsored by the U.S. Department of Energy.

  2. Biochemical and Structural Characterization of the Subclass B1 Metallo-β-Lactamase VIM-4 ▿

    PubMed Central

    Lassaux, Patricia; Traoré, Daouda A. K.; Loisel, Elodie; Favier, Adrien; Docquier, Jean-Denis; Sohier, Jean Sébastien; Laurent, Clémentine; Bebrone, Carine; Frère, Jean-Marie; Ferrer, Jean-Luc; Galleni, Moreno

    2011-01-01

    The metallo-β-lactamase VIM-4, mainly found in Pseudomonas aeruginosa or Acinetobacter baumannii, was produced in Escherichia coli and characterized by biochemical and X-ray techniques. A detailed kinetic study performed in the presence of Zn2+ at concentrations ranging from 0.4 to 100 μM showed that VIM-4 exhibits a kinetic profile similar to the profiles of VIM-2 and VIM-1. However, VIM-4 is more active than VIM-1 against benzylpenicillin, cephalothin, nitrocefin, and imipenem and is less active than VIM-2 against ampicillin and meropenem. The crystal structure of the dizinc form of VIM-4 was solved at 1.9 Å. The sole difference between VIM-4 and VIM-1 is found at residue 228, which is Ser in VIM-1 and Arg in VIM-4. This substitution has a major impact on the VIM-4 catalytic efficiency compared to that of VIM-1. In contrast, the differences between VIM-2 and VIM-4 seem to be due to a different position of the flapping loop and two substitutions in loop 2. Study of the thermal stability and the activity of the holo- and apo-VIM-4 enzymes revealed that Zn2+ ions have a pronounced stabilizing effect on the enzyme and are necessary for preserving the structure. PMID:21149620

  3. Non-Linear Structural Dynamics Characterization using a Scanning Laser Vibrometer

    NASA Technical Reports Server (NTRS)

    Pai, P. F.; Lee, S.-Y.

    2003-01-01

    This paper presents the use of a scanning laser vibrometer and a signal decomposition method to characterize non-linear dynamics of highly flexible structures. A Polytec PI PSV-200 scanning laser vibrometer is used to measure transverse velocities of points on a structure subjected to a harmonic excitation. Velocity profiles at different times are constructed using the measured velocities, and then each velocity profile is decomposed using the first four linear mode shapes and a least-squares curve-fitting method. From the variations of the obtained modal \\ielocities with time we search for possible non-linear phenomena. A cantilevered titanium alloy beam subjected to harmonic base-excitations around the second. third, and fourth natural frequencies are examined in detail. Influences of the fixture mass. gravity. mass centers of mode shapes. and non-linearities are evaluated. Geometrically exact equations governing the planar, harmonic large-amplitude vibrations of beams are solved for operational deflection shapes using the multiple shooting method. Experimental results show the existence of 1:3 and 1:2:3 external and internal resonances. energy transfer from high-frequency modes to the first mode. and amplitude- and phase- modulation among several modes. Moreover, the existence of non-linear normal modes is found to be questionable.

  4. Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

    NASA Astrophysics Data System (ADS)

    Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

    2014-05-01

    The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

  5. Synthesis, structure, and spectroscopic characterization of three uranyl phosphates with unique structural units

    SciTech Connect

    Wylie, Ernest M.; Dawes, Colleen M.; Burns, Peter C.

    2012-12-15

    Single crystals of Zn{sub 4}(OH){sub 2}[(UO{sub 2})(PO{sub 4}){sub 2}(OH){sub 2}(H{sub 2}O)] (UZnP), Cs[(UO{sub 2})(HPO{sub 4})NO{sub 3}] (UCsP), and In{sub 3}[(UO{sub 2}){sub 2}(PO{sub 4}){sub 4}OH(H{sub 2}O){sub 6}].2H{sub 2}O (UInP) were obtained from hydrothermal reactions and have been structurally and chemically characterized. UZnP crystallizes in space group Pbcn, a=8.8817(7), b=6.6109(5), c=19.569(1) A; UCsP crystallizes in P-1, a=7.015(2), b=7.441(1), c=9.393(2) A, {alpha}=72.974(2), {beta}=74.261(2), {gamma}=79.498(2); and UInP crystallizes in P-1, a=7.9856(5), b=9.159(1), c=9.2398(6) A {alpha}=101.289(1), {beta}=114.642(1), {gamma}=99.203(2). The U{sup 6+} cations are present as (UO{sub 2}){sup 2+} uranyl ions coordinated by five O atoms to give pentagonal bipyramids. The structural unit in UZnP is a finite cluster containing a uranyl pentagonal bipyramid that shares corners with two phosphate tetrahedra. The structural unit in UCsP is composed of uranyl pentagonal bipyramids with one chelating nitrate group that are linked into chains by three bridging hydrogen phosphate tetrahedra. In UInP, the structural unit contains pairs of edge-sharing uranyl pentagonal bipyramids with two chelating phosphate tetrahedra that are linked into chains through two bridging phosphate tetrahedra. Indium octahedra link these uranyl phosphate chains into a 3-dimensional framework. All three compounds exhibit unique structural units that deviate from the typical layered structures observed in uranyl phosphate solid-state chemistry. - Graphical abstract: Three new uranyl phosphates with unique structural units are reported. Black-Small-Square Highlights: Black-Right-Pointing-Pointer Three new uranyl phosphates have been synthesized hydrothermally. Black-Right-Pointing-Pointer Single crystal analyses reveal unique structural units. Black-Right-Pointing-Pointer The dimensionality of these compounds deviate from typical U{sup 6+} layered structures.

  6. Structural and spectroscopic characterization of ettringite mineral -combined DFT and experimental study

    NASA Astrophysics Data System (ADS)

    Scholtzová, Eva; Kucková, Lenka; Kožíšek, Jozef; Tunega, Daniel

    2015-11-01

    The structure of the ettringite mineral was studied by means of FTIR spectroscopy and single crystal X-ray diffraction method. The experimental study was combined with the first principle calculations based on density functional theory (DFT) method. Predicted structural parameters (unit cell vectors and positions of heavy atoms) are in a very good agreement with the experimental data. Moreover, calculations also enabled to refine the positions of the hydrogen atoms not determined precisely by the single crystal X-ray measurement. The detailed analysis of the hydrogen bonds in the ettringite structure was performed and several groups of the hydrogen bonds were classified. It was found that the water molecules from the coordination sphere of Ca2+ cations act as proton donors in moderate O-H···O hydrogen bonds with SO 32- anions. Further, multiple O-H···O hydrogen bonds were identified among water molecules themselves. In addition, also hydroxyl groups from the [Al(OH)6]3- octahedral units are involved in the weak O-H···O hydrogen bonding with the water molecules. The calculated vibrational spectrum showed all typical features observed in the experimental FTIR spectrum. Moreover, performing the analysis of the calculated spectrum, all vibrational modes were distinguished and assigned. Such a complete analysis of the measured IR and/or Raman spectra is not fully possible, specifically for the region below 1500 cm-1, which is characterized by a complex curve with many overlapped bands. A comparison of the vibrational spectra of ettringite and thaumasite (mineral structurally similar to ettringite) revealed the origin of the most important differences between them.

  7. Methodology Using Inverse Methods for Pit Characterization in Multilayer Structures

    NASA Astrophysics Data System (ADS)

    Aldrin, John C.; Sabbagh, Harold A.; Sabbagh, Elias H.; Murphy, R. Kim; Concordia, Michael; Judd, David R.; Lindgren, Eric; Knopp, Jeremy

    2006-03-01

    This paper presents a methodology incorporating ultrasonic and eddy current data and NDE models to characterize pits in first and second layers. Approaches such as equivalent pit dimensions, approximate probe models, and iterative inversion schemes were designed to improve the reliability and speed of inverse methods for second layer pit characterization. A novel clutter removal algorithm was developed to compensate for coherent background noise. Validation was achieved using artificial and real pitting corrosion samples.

  8. Fabrication and characterization of metallic quasi-periodic structures.

    PubMed

    Wang, Yongjin

    2008-01-21

    A variety of intriguing interference patterns are generated as a template to create metallic quasi-periodic structures using our robust experimental setup. A combination of thermal evaporation and lift-off process, the 2D metallic quasi-periodic structures are generated, a twelve-fold symmetry structure can be clearly observed in fabricated structures with four exposures. The excitation of surface plasmon (SP) resonances, which are determined by the geometry of metallic structures, the incident angle alpha, and the refractive index n(d) of the adjacent dielectric medium, is demonstrated in the optical transmission experiments. The optical transmission of metallic quasi-periodic structures can be tuned by varying the refractive index n(d), changing the period a and altering the incident angle alpha. The experimental results agree well with the predication for SP resonances. It's the first step to investigate the interesting optical properties of metallic quasi-periodic structures.

  9. Structural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza A virus.

    PubMed

    Li, Qing; Sun, Xiaoman; Li, Zhixin; Liu, Yue; Vavricka, Christopher J; Qi, Jianxun; Gao, George F

    2012-11-13

    The recent discovery of the unique genome of influenza virus H17N10 in bats raises considerable doubt about the origin and evolution of influenza A viruses. It also identifies a neuraminidase (NA)-like protein, N10, that is highly divergent from the nine other well-established serotypes of influenza A NA (N1-N9). The structural elucidation and functional characterization of influenza NAs have illustrated the complexity of NA structures, thus raising a key question as to whether N10 has a special structure and function. Here the crystal structure of N10, derived from influenza virus A/little yellow-shouldered bat/Guatemala/153/2009 (H17N10), was solved at a resolution of 2.20 Å. Overall, the structure of N10 was found to be similar to that of the other known influenza NA structures. In vitro enzymatic assays demonstrated that N10 lacks canonical NA activity. A detailed structural analysis revealed dramatic alterations of the conserved active site residues that are unfavorable for the binding and cleavage of terminally linked sialic acid receptors. Furthermore, an unusual 150-loop (residues 147-152) was observed to participate in the intermolecular polar interactions between adjacent N10 molecules of the N10 tetramer. Our study of influenza N10 provides insight into the structure and function of the sialidase superfamily and sheds light on the molecular mechanism of bat influenza virus infection.

  10. Chord Splicing & Joining Detail; Chord & CrossBracing Joint Details; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Chord Splicing & Joining Detail; Chord & Cross-Bracing Joint Details; Cross Bracing Center Joint Detail; Chord & Diagonal Joint Detail - Vermont Covered Bridge, Highland Park, spanning Kokomo Creek at West end of Deffenbaugh Street (moved to), Kokomo, Howard County, IN

  11. Arch & Chord Joint Detail; Crossbracing Center Joint Detail; Chord, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Arch & Chord Joint Detail; Crossbracing Center Joint Detail; Chord, Panel Post, Tie & Diagonal Brace Joint Detail; Chord, Panel Post, Tie & Crossbracing Joint Detail - Dunlapsville Covered Bridge, Spanning East Fork Whitewater River, Dunlapsville, Union County, IN

  12. Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea.

    PubMed

    Kopecky, Vladimir; Kohoutova, Jaroslava; Lapkouski, Mikalai; Hofbauerova, Katerina; Sovova, Zofie; Ettrichova, Olga; González-Pérez, Sergio; Dulebo, Alexander; Kaftan, David; Smatanova, Ivana Kuta; Revuelta, Jose L; Arellano, Juan B; Carey, Jannette; Ettrich, Rüdiger

    2012-01-01

    Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR) exploits an intermediate phase that, although nominally "dry," has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å) x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein.

  13. Bis-benzimidazol-appended binucleating porphyrin ligands: synthesis, characterization, and x-ray structure

    SciTech Connect

    Larsen, N.G.; Boyd, P.D.W.; Rodgers, S.J.; Wuenschell, G.E.; Koch, C.A.; Rasmussen, S.; Tate, J.R.; Erler, B.S.; Reed, C.A.

    1986-10-29

    The synthesis and characterization of some new binucleating tetraarylporphyrin ligands is reported. The potentially most useful example is ..cap alpha..,..cap alpha..,5-15-bis(N-(2-methylbenzimidazolyl) acetamidophenyl)-..cap alpha..,..cap alpha..,10-20-bis(pivalamidophenyl)porphine (8). The ligands have two appended benzimidazole arms which are designed to chelate a second metal directly above the porphyrin. The synthetic methodology for obtaining both the 5,15 (i.e. trans) and the 5,10 (i.e., cis) bis-appended ligand from an ..cap alpha.., ..cap alpha.., ..cap alpha.., ..cap alpha..,5,10,15,20 tetra-functionalized starting material is described in detail. A key design feature of the ligand system is amenability to single-crystal x-ray structure determination and this is demonstrated with an x-ray structure of a copper(II) complex. Crystal data for CuC/sub 74/H/sub 66/N/sub 12/O/sub 3/1.5 (diethyl ether) toluene are the following: monoclinic, C2/c, a = 31.240 (4) A, b = 16.769 (5) A, c = 35.199 (4) A, ..beta.. = 121.4 (1)/sup 0/; R = 0.0826, R/sub W/ = 0.0826. H bonding between the benzimidazole moieties and the pivalamido pickets is seen to determine the structural disposition of the appendages lying above the porphyrin ring. Iron(III) porphyrin complexes of these new ligands exist in a hydroxo monomer form as well as the familiar ..mu..-oxo dimer form.

  14. Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features

    SciTech Connect

    Chatfield, M.J.; La Mar, G.N.; Kauten, R.J.

    1987-11-03

    The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by /sup 1/H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and /sup 1/H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only /sup 1/H NMR clearly distinguishes all three ferric isomers. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first /sup 1/H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albiet to a smaller extent.

  15. Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl-Prolyl Isomerases

    SciTech Connect

    Davis, Tara L.; Walker, John R.; Campagna-Slater, Valérie; Finerty, Jr., Patrick J.; Paramanathan, Ragika; Bernstein, Galina; MacKenzie, Farrell; Tempel, Wolfram; Ouyang, Hui; Lee, Wen Hwa; Eisenmesser, Elan Z.; Dhe-Paganon, Sirano

    2011-12-14

    Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure:function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform

  16. Structural characterization of magnesium silicate hydrate: towards the design of eco-sustainable cements.

    PubMed

    Tonelli, M; Martini, F; Calucci, L; Fratini, E; Geppi, M; Ridi, F; Borsacchi, S; Baglioni, P

    2016-02-28

    Magnesium-based cement is one of the most interesting eco-sustainable alternatives to standard cementitious binders. The reasons for the interest towards this material are twofold: (i) its production process, using magnesium silicates, brine or seawater, dramatically reduces CO2 emissions with respect to Portland cement production, and (ii) it is very well suited to applications in radioactive waste encapsulation. In spite of its potential, assessment of the structural properties of its binder phase (magnesium silicate hydrate or M-S-H) is far from complete, especially because of its amorphous character. In this work, a comprehensive structural characterization of M-S-H was obtained using a multi-technique approach, including a detailed solid-state NMR investigation and, in particular, for the first time, quantitative (29)Si solid-state NMR data. M-S-H was prepared through room-temperature hydration of highly reactive MgO and silica fume and was monitored for 28 days. The results clearly evidenced the presence in M-S-H of "chrysotile-like" and "talc-like" sub-nanometric domains, which are approximately in a 1 : 1 molar ratio after long-time hydration. Both these kinds of domains have a high degree of condensation, corresponding to the presence of a small amount of silanols in the tetrahedral sheets. The decisive improvement obtained in the knowledge of M-S-H structure paves the way for tailoring the macroscopic properties of eco-sustainable cements by means of a bottom-up approach.

  17. Fabrication, characterization, and simulation of photonic bandgap structures

    NASA Astrophysics Data System (ADS)

    Wang, Hao

    Photonic bandgap (PBG) structures are artificial materials which are featured with periodically changed refractive index having a periodicity in the range of optical wavelengths. The studies in PBG structures are making rapid progress. However, the investigations of three-dimensional (3-D) PBG structures are still challenging. In this work, laser-assisted fabrication of 3-D PBG structures based on self-assembled silica colloidal crystals was developed. 3-D PBG structures were fabricated by laser-assisted nano-imprinting and laser-assisted chemical vapor deposition (LCVD), based on the self-assembled silica colloidal crystals. Silica colloidal crystals were self-assembled on silicon substrates using isothermal heating evaporation-induced self-assembly. To infiltrate the silica colloidal crystals, the laser-assisted imprinting technique was used using a short pulse (23 ns pulse duration) of a KrF excimer laser. The nanosecond laser pulse instantaneously melted the silicon substrates, which infiltrated and solidified over the assembled silica particles on the substrates. By removing silica particles embedded in the silicon using hydrofluoric acid, inverseopal PBG structures were produced. In the LCVD technique, a continuous-wave Nd:YAG laser (1.064 mum wavelength) and a CO2 laser (10.6 mum wavelength) were used as the energy source. Silica-core-silicon-shell PBG structures were obtained. This technique is capable of fabricating structures with various PBGs by obtaining different silicon-shell thickness with different LCVD parameters. Both theoretical calculations and experimental measurements to investigate the optical properties of the PBG structures were carried out. Spectroscopic ellipsometry was used to identify PBGs. The plain-wave expansion (PWE) method was used to calculate the photonic-band diagrams of the structures, which agreed with the experimental results. The calculation also provided fitting results of the Si-shell thicknesses. To investigate the

  18. 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.

  19. Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of Vulnerability

    SciTech Connect

    Hansman, Grant S.; Biertümpfel, Christian; Georgiev, Ivelin; McLellan, Jason S.; Chen, Lei; Zhou, Tongqing; Katayama, Kazuhiko; Kwong, Peter D.

    2011-10-10

    Noroviruses are the dominant cause of outbreaks of gastroenteritis worldwide, and interactions with human histo-blood group antigens (HBGAs) are thought to play a critical role in their entry mechanism. Structures of noroviruses from genogroups GI and GII in complex with HBGAs, however, reveal different modes of interaction. To gain insight into norovirus recognition of HBGAs, we determined crystal structures of norovirus protruding domains from two rarely detected GII genotypes, GII.10 and GII.12, alone and in complex with a panel of HBGAs, and analyzed structure-function implications related to conservation of the HBGA binding pocket. The GII.10- and GII.12-apo structures as well as the previously solved GII.4-apo structure resembled each other more closely than the GI.1-derived structure, and all three GII structures showed similar modes of HBGA recognition. The primary GII norovirus-HBGA interaction involved six hydrogen bonds between a terminal {alpha}fucose1-2 of the HBGAs and a dimeric capsid interface, which was composed of elements from two protruding subdomains. Norovirus interactions with other saccharide units of the HBGAs were variable and involved fewer hydrogen bonds. Sequence analysis revealed a site of GII norovirus sequence conservation to reside under the critical {alpha}fucose1-2 and to be one of the few patches of conserved residues on the outer virion-capsid surface. The site was smaller than that involved in full HBGA recognition, a consequence of variable recognition of peripheral saccharides. Despite this evasion tactic, the HBGA site of viral vulnerability may provide a viable target for small molecule- and antibody-mediated neutralization of GII norovirus.

  20. Detailed structure of the low-energy magnetic dispersion of the diagonal incommensurate phase in La1.975Sr0.025CuO4

    NASA Astrophysics Data System (ADS)

    Matsuda, M.; Fernandez-Baca, J. A.; Fujita, M.; Yamada, K.; Tranquada, J. M.

    2011-09-01

    Inelastic neutron scattering experiments have been performed on lightly doped La1.975Sr0.025CuO4, which contains a hole concentration slightly higher than the critical concentration for three-dimensional long-range antiferromagnetic order. We previously found that the magnetic excitation spectrum in the insulating phase with a diagonal incommensurate spin modulation has similarities to that in the superconducting regime, where the spin modulation is bond parallel. In this study, we investigate the excitations in detail around Ecross, at which the excitations become most nearly commensurate. It is found that both the magnitude and the anisotropy of the momentum width of the excitations change abruptly at Ecross. Our experimental results suggest that the magnetic excitations rising from the pair of (diagonally) incommensurate wave vectors merge at Ecross into isotropic excitations.

  1. Molecular characterization and population structure of Blueberry mosaic associated virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Blueberry mosaic disease was first described in the 1950s but the causal agent has not been characterized to date. Next generation sequencing was employed in the identification of the causal agent and an undescribed ophiovirus, tentatively named as Blueberry mosaic associated virus (BlMaV), was dete...

  2. Characterization of flow-induced structures in carbon nanotube suspensions

    NASA Astrophysics Data System (ADS)

    Khalkhal, Fatemeh

    Carbon nanotubes (CNTs) are fibre-like nano-particles with many different applications. Due to their high specific surface area, high electric current density, thermal stability and excellent mechanical properties, they are used to reinforce physical properties of polymer matrices. The macroscopic properties of suspensions are inherited from their properties at micron and sub-micron scales. The suspensions structure can be easily influenced by many parameters such as the extent of external shear forces, the suspension concentration, temperature, the particles specifications, etc. This makes the study of the suspension structure a very challenging task and has been the subject of interest to many researchers. In this thesis, the structure of a model carbon nanotube suspension dispersed in an epoxy is studied by employing a set of rheological methods, scaling and fractal theories and a structural thixotropic model. The effect of flow history on linear viscoelastic properties of suspensions and the evolution of structure upon cessation of shear flow has been studied over a wide range of pre-shearing rates, concentration and temperature. The results of these analyses are as follows. The effect of flow history is more pronounced on the suspensions structure in dilute and semi-dilute concentration regimes. By pre-shearing at low rates, more inter-particle entanglements were induced, which resulted in reduction of rheological percolation thresholds. After cessation of shear flow, for dilute and semi-dilute suspensions, the formed metastable structures were distinguishable by different storage moduli, which were inversely related to the rate of pre-shearing. However, for the concentrated suspensions, the formed metastable structures had an approximately equal storage modulus regardless of the rate of the applied pre-shearing. It was shown that the rate of formation of these metastable structures was enhanced by increasing concentration. Furthermore, the rate of structure

  3. Structural Characterization of Cationic Liposomes Loaded with Sugar-Based Carboranes

    PubMed Central

    Ristori, Sandra; Oberdisse, Julian; Grillo, Isabelle; Donati, Alessandro; Spalla, Olivier

    2005-01-01

    In this article we report the physicochemical characterization of cationic liposomes loaded with orthocarborane and two of its sugar-containing derivatives. Carboranes are efficient boron delivery agents in boron neutron capture therapy, an anti-cancer treatment based on neutron absorption by 10B nuclei. Cationic liposomes were prepared using the positively charged DOTAP and the zwitterionic DOPE, as a helper lipid. These liposomes are currently used in gene therapy for their ability in targeting the cell nucleus; therefore they can be considered appropriate vectors for boron neutron capture therapy, in the quest of reducing the high boron amount that is necessary for successful cancer treatment. Boron uptake was determined by an original in situ method, based on neutron absorption. The structural properties of the loaded liposomes were studied in detail by the combined use of small angle x-ray scattering and small angle neutron scattering. These techniques established the global shape and size of liposomes and their bilayer composition. The results were discussed in term of molecular properties of the hosted drugs. Differences found in the insertion modality were correlated with the preparation procedure or with the specific shape and lipophilic-hydrophilic balance of each carborane. PMID:15489297

  4. Structure-from-Motion Approach for Characterization of Bioerosion Patterns Using UAV Imagery

    PubMed Central

    Genchi, Sibila A.; Vitale, Alejandro J.; Perillo, Gerardo M. E.; Delrieux, Claudio A.

    2015-01-01

    The aim of this work is to evaluate the applicability of the 3D model obtained through Structure-from-Motion (SFM) from unmanned aerial vehicle (UAV) imagery, in order to characterize bioerosion patterns (i.e., cavities for roosting and nesting) caused by burrowing parrots on a cliff in Bahía Blanca, Argentina. The combined use of SFM-UAV technology was successfully applied for the 3D point cloud model reconstruction. The local point density, obtained by means of a sphere of radius equal to 0.5 m, reached a mean value of 9749, allowing to build a high-resolution model (0.013 m) for resolving fine spatial details in topography. To test the model, we compared it with another point cloud dataset which was created using a low cost do-it-yourself terrestrial laser scanner; the results showed that our georeferenced model had a good accuracy. In addition, an innovative method for the detection of the bioerosion features was implemented, through the processing of data provided by SFM like color and spatial coordinates (particularly the y coordinate). From the 3D model, we also derived topographic calculations such as slope angle and surface roughness, to get associations between the surface topography and bioerosion features. PMID:25658392

  5. Structure-from-motion approach for characterization of bioerosion patterns using UAV imagery.

    PubMed

    Genchi, Sibila A; Vitale, Alejandro J; Perillo, Gerardo M E; Delrieux, Claudio A

    2015-02-04

    The aim of this work is to evaluate the applicability of the 3D model obtained through Structure-from-Motion (SFM) from unmanned aerial vehicle (UAV) imagery, in order to characterize bioerosion patterns (i.e., cavities for roosting and nesting) caused by burrowing parrots on a cliff in Bahía Blanca, Argentina. The combined use of SFM-UAV technology was successfully applied for the 3D point cloud model reconstruction. The local point density, obtained by means of a sphere of radius equal to 0.5 m, reached a mean value of 9749, allowing to build a high-resolution model (0.013 m) for resolving fine spatial details in topography. To test the model, we compared it with another point cloud dataset which was created using a low cost do-it-yourself terrestrial laser scanner; the results showed that our georeferenced model had a good accuracy. In addition, an innovative method for the detection of the bioerosion features was implemented, through the processing of data provided by SFM like color and spatial coordinates (particularly the y coordinate). From the 3D model, we also derived topographic calculations such as slope angle and surface roughness, to get associations between the surface topography and bioerosion features.

  6. Sizing Single Cantilever Beam Specimens for Characterizing Facesheet/Core Peel Debonding in Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.

    2010-01-01

    This technical publication details part of an effort focused on the development of a standardized facesheet/core peel debonding test procedure. The purpose of the test is to characterize facesheet/core peel in sandwich structure, accomplished through the measurement of the critical strain energy release rate associated with the debonding process. Following an examination of previously developed tests and a recent evaluation of a selection of these methods, a single cantilever beam (SCB) specimen was identified as being a promising candidate for establishing such a standardized test procedure. The objective of the work described here was to begin development of a protocol for conducting a SCB test that will render the procedure suitable for standardization. To this end, a sizing methodology was developed to ensure appropriate SCB specimen dimensions are selected for a given sandwich system. Application of this method to actual sandwich systems yielded SCB specimen dimensions that would be practical for use. This study resulted in the development of a practical SCB specimen sizing method, which should be well-suited for incorporation into a standardized testing protocol.

  7. Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas.

    PubMed

    Chong, Lauren C; Twa, David D W; Mottok, Anja; Ben-Neriah, Susana; Woolcock, Bruce W; Zhao, Yongjun; Savage, Kerry J; Marra, Marco A; Scott, David W; Gascoyne, Randy D; Morin, Ryan D; Mungall, Andrew J; Steidl, Christian

    2016-09-01

    Programmed death ligands (PDLs) are immune-regulatory molecules that are frequently affected by chromosomal alterations in B-cell lymphomas. Although PDL copy-number variations are well characterized, a detailed and comprehensive analysis of structural rearrangements (SRs) and associated phenotypic consequences is largely lacking. Here, we used oligonucleotide capture sequencing of 67 formalin-fixed paraffin-embedded tissues derived from primary B-cell lymphomas and 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24.1; harboring PDL1/CD274 and PDL2/PDCD1LG2). We describe 36 novel PDL SRs, including 17 intrachromosomal events (inversions, duplications, deletions) and 19 translocations involving BZRAP-AS1, CD44, GET4, IL4R, KIAA0226L, MID1, RCC1, PTPN1 and segments of the immunoglobulin loci. Moreover, analysis of the precise chromosomal breakpoints reveals 2 distinct cluster breakpoint regions (CBRs) within either CD274 (CBR1) or PDCD1LG2 (CBR2). To determine the phenotypic consequences of these SRs, we performed immunohistochemistry for CD274 and PDCD1LG2 on primary pretreatment biopsies and found that PDL SRs are significantly associated with PDL protein expression. Finally, stable ectopic expression of wild-type PDCD1LG2 and the PDCD1LG2-IGHV7-81 fusion showed, in coculture, significantly reduced T-cell activation. Taken together, our data demonstrate the complementary utility of fluorescence in situ hybridization and capture sequencing approaches and provide a classification scheme for PDL SRs with implications for future studies using PDL immune-checkpoint inhibitors in B-cell lymphomas.

  8. Structure of the human FOXO4-DBD-DNA complex at 1.9 Å resolution reveals new details of FOXO binding to the DNA.

    PubMed

    Boura, Evzen; Rezabkova, Lenka; Brynda, Jiri; Obsilova, Veronika; Obsil, Tomas

    2010-12-01

    FOXO4 is a member of the FOXO subgroup of forkhead transcription factors that constitute key components of a conserved signalling pathway that connects growth and stress signals to transcriptional control. Here, the 1.9 Å resolution crystal structure of the DNA-binding domain of human FOXO4 (FOXO4-DBD) bound to a 13 bp DNA duplex containing a FOXO consensus binding sequence is reported. The structure shows a similar recognition of the core sequence as has been shown for two other FOXO proteins. Helix H3 is docked into the major groove and provides all of the base-specific contacts, while the N-terminus and wing W1 make additional contacts with the phosphate groups of DNA. In contrast to other FOXO-DBD-DNA structures, the loop between helices H2 and H3 has a different conformation and participates in DNA binding. In addition, the structure of the FOXO4-DBD-DNA complex suggests that both direct water-DNA base contacts and the unique water-network interactions contribute to FOXO-DBD binding to the DNA in a sequence-specific manner.

  9. Tetragonal-strain-induced local structural modifications in InAsxP1-x/InP superlattices: A detailed x-ray-absorption investigation

    NASA Astrophysics Data System (ADS)

    Pascarelli, S.; Boscherini, F.; Lamberti, C.; Mobilio, S.

    1997-07-01

    We report a comprehensive investigation of the local structure around As in thin InAsxP1-x strained layers in InAsxP1-x/InP superlattices by fluorescence-detected x-ray-absorption fine structure; seven superlattice samples are studied as a function of composition, and compared to six unstrained, bulk samples of similar composition. Contributions up to the third coordination shell around As are clearly visible in the spectra, and are analyzed taking into account important multiple-scattering contributions. Results show that structural modifications due to tetragonal distortion appear mainly in the second and third coordination shells, while nearest-neighbor bond lengths remain closer to the values in unstrained bulk alloys. This implies that in semiconductor alloys tetragonal strain accommodation is mainly obtained through bond-angle distortions, in analogy to the situation in bulk pseudobinary alloys. A model which combines macroscopic elastic theory and the known local structure in bulk pseudobinary alloys is presented, and is found to fit the data very well.

  10. A Structurally Characterized Organometallic Plutonium(IV) Complex.

    PubMed

    Apostolidis, Christos; Walter, Olaf; Vogt, Jochen; Liebing, Phil; Maron, Laurent; Edelmann, Frank T

    2017-03-30

    The blood-red plutonocene complex Pu(1,3-COT'')(1,4-COT'') (4; COT''=η(8) -bis(trimethylsilyl)cyclooctatetraenyl) has been synthesized by oxidation of the anionic sandwich complex Li[Pu(1,4-COT'')2 ] (3) with anhydrous cobalt(II) chloride. The first crystal structure determination of an organoplutonium(IV) complex revealed an asymmetric sandwich structure for 4 where one COT'' ring is 1,3-substituted while the other retains the original 1,4-substitution pattern. The electronic structure of 4 has been elucidated by a computational study, revealing a probable cause for the unexpected silyl group migration.

  11. Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase.

    PubMed

    Girish, Tavarekere S; Sharma, Eshita; Gopal, B

    2008-08-20

    Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.

  12. Structural Characterization and Impedance Spectroscopy of Substituted, Fused-Ring Organic Semiconductors

    NASA Astrophysics Data System (ADS)

    Shaw, Charles Michael

    Organic materials present a number of advantages over silicon that make them ideal candidates for modest performance devices like active matrix backplanes and RFID tags. The work detailed here describes both structural characterization of promising new materials, as well as the adaptation of impedance spectroscopy techniques to the study of organic transistors. Unit cells and solution casting behavior for dioctyl- and didodecyl-pentathienoacene are presented. Dioctyl pentathienoacene has an orthorhombic lattice with parameters a = 1.15 nm, b = 0.43 nm and c = 3.05 nm. Didodecyl pentathienoacene has an monoclinic lattice with parameters gamma = 92.2°, a = 1.10 urn, b = 0.42 nm and c = 3.89 nm. Additionally, thermotropic phase behavior is detailed. Both materials exhibit a "side chain melting" transition---characterized by a dramatic unit cell contraction of more than 20%---and smectic C liquid crystal phases. The side chain melting transition shows similarity to phase transitions elicited by exposing these materials to high energy electron flux. In both cases, disorder in the substitutions results in new phases for these materials. Dioctyl-pentathienoacene also exhibits a unique phase, which is intermediately ordered and shows a threefold increase in critical dose over the as-cast phase. Impedance spectroscopy of triisopropylsilyl pentacene transistors suggests these devices are well fit by a Voigt model equivalent circuit. The gate bias dependent resistor represents the channel conductance and the capacitor represents the drain-gate and source-gate capacitances. This in turn suggests that conduction occurs through delocalized states available in ordered regions, with disordered regions contributing localized, immobile states. Impedance spectroscopy of poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) shows similar behavior. The use of variable temperature impedance spectroscopy is also demonstrated. This technique is used to measure the reduction in trap

  13. Detailed structure and tectonics of the Ninetyeast Ridge near Site ODP 758 (on new geophysical data from KNOX06RR cruise of R/V Roger Revelle)

    NASA Astrophysics Data System (ADS)

    Levchenko, O.; Eisin, A. E.; Ivanenko, A. N.; Marinova, J. G.; Paul, C. F.; Sborshchikov, I. M.; Sager, W. W.

    2008-12-01

    Detailed geophysical survey was carried out during the NSF-funded KNOX06RR cruise of R/V Roger Revelle in July 2007 over the ~70×70 km area near ODP Site 758, the northern Ninetyeast Ridge (NER). In addition to multibeam echo-sounder bathymetry, 3.5 kHz echo-sounder profiles, magnetic, and gravity data, high-resolution multichannel seismic reflection data were collected on eight orthogonal profiles of total length ~270 km. Large NE-trending depressions with complicated horst and graben morphology dominate the whole detailed survey area. The numerous basement faults extend upward into overlying sediments filling out these depressions. Thickness of the sedimentary fill is highly variable due to very rough basement topography, and is up to 800 m maximum. This fill is divided in two clear sedimentary layers: transparent pelagic sediments above and stratified shallow-water ones below. Two high ~400-450 m isometric seamounts extend from the surrounding NER seafloor. High-resolution seismic records show that these igneous basement highs are covered by thin transparent pelagic sediments which hamper the dredging of volcanic rocks. Seismic stratigraphy analyses for sedimentary cover over the seamounts buried slopes suggest that they seem to be recent volcanoes superimposed on the main NER edifice. Both volcanoes are clearly delineated in the constructed map of total anomaly magnetic field. Since water depths are ~2.5 km above these seamounts, the lower edge of the magnetic body in these volcanoes is situated deep at ~7 km under sea level. That appears to represent deep roots of the volcanoes. Preliminary magnetic modeling shows that they were generated during negative chron of the geomagnetic scale rather not long ago and not far from their present location, seeming to confirm the inference that these volcanoes are recent in origin. In general, one may assume a secondary phase of magmatic activity on the NER. It is important to reveal, any recent phase of tectonic and

  14. Structural and Kinetic Characterization of Escherichia coli TadA, the Wobble-Specific tRNA Deaminase

    SciTech Connect

    Kim,J.; Malashkevich, V.; Roday, S.; Lisbin, M.; Schramm, V.; Almo, S.

    2006-01-01

    The essential tRNA-specific adenosine deaminase catalyzes the deamination of adenosine to inosine at the wobble position of tRNAs. This modification allows for a single tRNA species to recognize multiple synonymous codons containing A, C, or U in the last (3'-most) position and ensures that all sense codons are appropriately decoded. We report the first combined structural and kinetic characterization of a wobble-specific deaminase. The structure of the Escherichia coli enzyme clearly defines the dimer interface and the coordination of the catalytically essential zinc ion. The structure also identifies the nucleophilic water and highlights residues near the catalytic zinc likely to be involved in recognition and catalysis of polymeric RNA substrates. A minimal 19 nucleotide RNA stem substrate has permitted the first steady-state kinetic characterization of this enzyme (k{sub cat} = 13 {+-} 1 min{sup -1} and K{sub M} = 0.83 {+-} 0.22 {micro}M). A continuous coupled assay was developed to follow the reaction at high concentrations of polynucleotide substrates (>10 {micro}M). This work begins to define the chemical and structural determinants responsible for catalysis and substrate recognition and lays the foundation for detailed mechanistic analysis of this essential enzyme.

  15. LF460 detail design

    NASA Technical Reports Server (NTRS)

    1971-01-01

    This is the final technical report documenting the detail design of the LF460, and advanced turbotip lift fan intended for application with the YJ97-GE-100 turbojet jet generator to a V/STOL transport research aircraft. Primary objective of the design was to achieve a low noise level while maintaining the high thrust/weight ratio capability of a high pressure ratio lift fan. Report covers design requirements and summarizes activities and final results in the areas of aerodynamic and mechanical design, component and system performance, acoustic features and final noise predictions.

  16. Structural Characterization of a Hybrid Carrageenan-Like Sulfated Galactan from a Marine Red Alga Furcellaria lumbricalis.

    PubMed

    Lv, Youjing; Yang, Bo; Zhao, Xia; Zhang, Junzeng; Yu, Guangli

    2015-01-01

    Carrageenans are sulfated galactan isolated from marine red algae with different disaccharide forms. There are also some hybrid carrageenan-like oligomers, which are reported to possess a number of bioactivities. Here, we describe a method to study the structural characterization of a carrageenan-like sulfated galactan FB1 extracted from the red seaweed Furcellaria lumbricalis. We show the process of the general analysis of FB1, including the molecular weight, sulfate content, total sugar content, protein content, and 3,6-anhydrogalactose (3,6-AnG) content analyses. The fine structure identification methods, including desulfation and methylation, nuclear magne