Structural Analysis of Binding Determinants of Salmonella typhimurium Trehalose-6-phosphate Phosphatase Using Ground-State Complexes
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99 GENERAL AND MISCELLANEOUS↗
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High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin–Iron Complexes: Novel Pipeline and Complex Structures
Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools. The protocol was used for investigating the Fe complexes formed by model compounds of lignin-derived organic ligands, namely, caffeic acid (CA), p-coumaric acid (CMA), vanillin (VNL), and cinnamic acid (CNA). Isotopologue analysis of 54/56 Fe was used to screen out the potential UHPLC-HRMS (m/z) features for complexes formed between organic ligands and Fe, with multiple features captured for CA, CMA, VNL, and CNA when 35/37 Cl isotopologue analysis was used as supplementary evidence for the complexes with Cl. MS/MS spectra, fragment analysis, and structure prediction with SIRIUS were used to annotate the structures of mono/bidentate mono/biligand complexes. The analysis determined the structures of monodentate and bidentate complexes of FeL x Cl y (L: organic ligand, x = 1–4, y = 0–3) formed by model compounds. The protocol developed in this study can be used to identify unknown organic ligands occurring in complex environmental samples and shed light on the molecular-level processes governing the stability of the SOC.
54 ENVIRONMENTAL SCIENCES↗
Efficient Analysis of Complex Structures
Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).
Kapania, Rakesh K.↗
Complex structure due to As bonding and interplay with electronic structure in superconducting BaNi 2 As 2
BaNi 2 As 2 is a superconductor chemically related to the Fe-based superconductors, with a complex and poorly understood structural phase transition. We show, based on first-principles calculations, that, in fact, there are two distinct competing structures. These structures are different from the electronic, transport, and bonding points of view but are close in energy. These arise due to complex As bonding patterns and drive distortions of the Ni layers. This is supported by photoemission experiments. This is very distinct from views of the distortion as being primarily driven by electrons at the Fermi surface as in a classical charge density wave, or by correlated electron physics associated with the Ni d electrons and the Ni d orbitals. The structural distortion, although connected with As does lead to an interplay of electronic and structural behavior including induced anisotropic electronic transport. Here, the local bonding nature of the instabilities and the competition between distortions is discussed in the context of the complex behavior observed in BaNi 2 As 2 samples.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structural studies of the coiled-coil domain of TRIM75 reveal a tetramer architecture facilitating i
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Lou, Xiaohua↗
Disturbance has variable effects on the structural complexity of a temperate forest landscape
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54 ENVIRONMENTAL SCIENCES↗
Robustness with real parametric and structured complex uncertainty
The problem of robust stability and performance in feedback control systems with n real (possibly related) uncertain parameters and structured unmodeled dynamics (the latter taking the form of m complex blocks dynamic uncertainties) is considered. A robustness margin rm is defined with respect to such model uncertainty structure and an algorithm is developed to compute it. Robust stability and performance are characterized in terms of r sub m or the structured singular value mu. An iterative procedure using the above algorithm is given to compute tight bounds on k sub m and mu. These bounds are exact for the case m = 3 or less.
Pena, Ricardo S. Sanchez↗
Structurally complex and highly active RNA ligases derived from random RNA sequences
Seven families of RNA ligases, previously isolated from random RNA sequences, fall into three classes on the basis of secondary structure and regiospecificity of ligation. Two of the three classes of ribozymes have been engineered to act as true enzymes, catalyzing the multiple-turnover transformation of substrates into products. The most complex of these ribozymes has a minimal catalytic domain of 93 nucleotides. An optimized version of this ribozyme has a kcat exceeding one per second, a value far greater than that of most natural RNA catalysts and approaching that of comparable protein enzymes. The fact that such a large and complex ligase emerged from a very limited sampling of sequence space implies the existence of a large number of distinct RNA structures of equivalent complexity and activity.
Non-NASA Center↗
Analysis and representation of complex structures in separated flows
We discuss our recent work on extraction and visualization of topological information in separated fluid flow data sets. As with scene analysis, an abstract representation of a large data set can greatly facilitate the understanding of complex, high-level structures. When studying flow topology, such a representation can be produced by locating and characterizing critical points in the velocity field and generating the associated stream surfaces. In 3D flows, the surface topology serves as the starting point. The 2D tangential velocity field near the surface of the body is examined for critical points. The tangential velocity field is integrated out along the principal directions of certain classes of critical points to produce curves depicting the topology of the flow near the body. The points and curves are linked to form a skeleton representing the 2D vector field topology. This skeleton provides a basis for analyzing the 3D structures associated with the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations. Integration origins are successively refined to produce stream surfaces. The map of the global topology is completed by generating those stream surfaces associated with 3D critical points.
Helman, James↗
Feasibility study in the application of optical signal analysis to non-destructive testing of complex structures
Advantages of the large time bandwidth product of optical processing are presented. Experiments were performed to study the feasibility of the use of optical spectral analysis for detection of flaws in structural elements excited by random noise. Photographic and electronic methods of comparison of complex spectra were developed. Limitations were explored, and suggestions for further work are offered.
Baker, B.↗
Tree mortality during long-term droughts is lower in structurally complex forest stands
Increasing drought frequency and severity in a warming climate threaten forest ecosystems with widespread tree deaths. Canopy structure is important in regulating tree mortality during drought, but how it functions remains controversial. Here, we show that the interplay between tree size and forest structure explains drought-induced tree mortality during the 2012-2016 California drought. Through an analysis of over one million trees, we find that tree mortality rate follows a “negative-positive-negative” piecewise relationship with tree height, and maintains a consistent negative relationship with neighborhood canopy structure (a measure of tree competition). Trees overshadowed by tall neighboring trees experienced lower mortality, likely due to reduced exposure to solar radiation load and lower water demand from evapotranspiration. Our findings demonstrate the significance of neighborhood canopy structure in influencing tree mortality and suggest that re-establishing heterogeneity in canopy structure could improve drought resiliency. Our study also indicates the potential of advances in remote-sensing technologies for silvicultural design, supporting the transition to multi-benefit forest management.
59 BASIC BIOLOGICAL SCIENCES↗
Complex structure of the Thaumasia region of Mars
The Thaumasia region was the first center of Tharsis tectonism, and it is the most complex and poorly understood. Therefore, a geologic map of the entire Thaumasia region (lat 15 deg to 50 deg S, long 50 deg to 115 deg), at 1:5,000,000 scale is being compiled. This region is mostly made up of the Thaumasia plateau, the highlands are fractured by Thaumasia, southern Claritas, Coracis, Melas, and Nectaris Fossae. Preliminary structural analysis of the most complexly faulted area in the region (the central part, at lat 30 deg to 45 deg S, long 80 deg to 100 deg) indicates that, unlike other regions of Mars, Thaumasia has undergone extensive deformation by both small- and large-scale extensional and compressional structures. These results indicate that the early (Noachian) style of tectonism commonly involved lithospheric-scale deformation, in contrast to most younger tectonism (which mainly affected the upper parts of the crust above mechanical discontinuities); this difference may be due to a weaker (and thus more readily deformable) early lithosphere in this region.
Tanaka, Kenneth L.↗
A simplified modal plotting technique for the representation of complex structural models
A plotting method has been developed that has proven to be useful in rapidly defining the mode shapes of a complex spacecraft. The reduction of the complex model to a simple stick plot is accomplished by augmenting the existing NASTRAN plot package with constrained plot elements. Both the existing NASTRAN modal plot package and the stick plots of a representative mode are presented for comparison. The NASTRAN plot package provides the capability of generating modal deformations (mode shapes) resulting from real eigenvalue analysis. These modal deformations of the structural model may be displayed in the deformed shape either alone or superimposed on the undeformed shape. Another available method of displaying the modal deformations is by means of displacement vectors at the grid points
Hanlein, S. L.↗
Complex structure of the supernova remnant HB 3
HB 3 is an old, large (84 pc diameter) supernova remnant associated with the W3 H II region/molecular cloud complex. Observations of the imaging proportional counter (IPC) onboard the Einstein X-ray astronomy satellite have been reprocessed to yield a contour map of X-ray brightness and spectra of various regions of this remnant. The measured IPC flux is 2.4 x 10 to the -11th ergs per sq cm per s, giving a 0.2-4 keV luminosity of 1.6 x 10 to the 35th ergs/s for a column densityof 6 x 10 to the 21st per sq cm. The measured X-ray temperatures reveal a decrease from center to limb of the remnant of 1-0.3 keV. HB 3 is in the late adiabatic blast-wave phase of evolution, 30,000 to 50,000 yr old and with an initial blast energy of 3 x 10 to the 50th ergs. The X-ray map is compared with available radio and optical images. In X-rays, HB 3 has two components - a diffuse emission inside the 84 pc radio remnant and a ring of emission at the center of 30 pc in diameter. The diffuse emission is similar to that from other supernova remnants which are moderately obscured (column density, nH approximately 10 to the 22nd per sq cm). Three possibilities for the origin of the ring are explored: (1) a second supernova remnant, (2) a shocked shell in the interstellar medium surrounding HB 3, and (3) reverse-shock heated ejecta. There is no hot neutron star within the remnant.
Leahy, D. A.↗
Anatomy of an agricultural antagonist: Feeding complex structure and function of three xylem sap‐feeding insects illuminated with synchrotron‐based 3D imaging
Abstract Many insects feed on xylem or phloem sap of vascular plants. Although physical damage to the plant is minimal, the process of insect feeding can transmit lethal viruses and bacterial pathogens. Disparities between insect‐mediated pathogen transmission efficiency have been identified among xylem sap‐feeding insects; however, the mechanistic drivers of these trends are unclear. Identifying and understanding the structural factors and associated integrated functional components that may ultimately determine these disparities are critical for managing plant diseases. Here, we applied synchrotron‐based X‐ray microcomputed tomography to digitally reconstruct the morphology of three xylem sap‐feeding insect vectors of plant pathogens: Graphocephala atropunctata (blue‐green sharpshooter; Hemiptera, Cicadellidae) and Homalodisca vitripennis (glassy‐winged sharpshooter; Hemiptera, Cicadellidae), and the spittlebug Philaenus spumarius (meadow spittlebug; Hemiptera, Aphrophoridae). The application of this technique revealed previously undescribed anatomical features of these organisms, such as key components of the salivary complex. The visualization of the 3D structure of the precibarial valve led to new insights into the mechanism of how this structure functions. Morphological disparities with functional implications between taxa were highlighted as well, including the morphology and volume of the cibarial dilator musculature responsible for extracting xylem sap, which has implications for force application capabilities. These morphological insights will be used to target analyses illuminating functional differences in feeding behavior.
3D imaging↗
Intrusive origin of the Sudbury Igneous Complex: Structural and sedimentological evidence
In recent years, many geoscientists have come to believe that the Sudbury event was exogenic rather than endogenic. Critical to a recent exogenic hypothesis is the impact melt origin of the Sudbury Igneous Complex (SIC). Such origin implies that the SIC was emplaced before deposition of the Whitewater Group, in contrast to origins in which the SIC postdates the lithification of the Onaping Formation. Structural and sedimentological evidence is summarized herein that supports an intrusion of the SIC after lithification of all Whitewater Group strata, and conflicts with the hypothesis advanced by other researchers.
Cowan, E. J.↗
Structural Complexities in Sodium Ion Conductive Antiperovskite Revealed by Cryogenic Transmission Electron Microscopy
Here we use low-dose cryogenic transmission electron microscopy (cryo-TEM) to investigate the atomic-scale structure of antiperovskite Na 2 NH 2 BH 4 crystals by preserving the room-temperature cubic phase and carefully monitoring the electron dose. Via quantitative analysis of electron beam damage using selected area electron diffraction, we find cryogenic imaging provides 6-fold improvement in beam stability for this solid electrolyte. Cryo-TEM images obtained from flat crystals revealed the presence of a new, long-range-ordered supercell with a cubic phase. The supercell exhibits doubled unit cell dimensions of 9.4 Å × 9.4 Å as compared to the cubic lattice structure revealed by X-ray crystallography of 4.7 Å × 4.7 Å. The comparison between the experimental image and simulated potential map indicates the origin of the supercell is a vacancy ordering of sodium atoms. This work demonstrates the potential of using cryo-TEM imaging to study the atomic-scale structure of air- and electron-beam-sensitive antiperovskite-type solid electrolytes.
36 MATERIALS SCIENCE↗