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At least 325 records · Page 18

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Identifying candidate structured RNAs in CRISPR operons

Noncoding RNAs with secondary structures play important roles in CRISPR-Cas systems. Many of these structures likely remain undiscovered. We used a large-scale comparative genomics approach to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems. A number of these were found to overlap with coding genes, including palindromic candidates that overlapped with a variety of Cas genes in type I and III systems. Among these 156 candidates, we identified 46 new models of CRISPR direct repeats and 1 tracrRNA. This tracrRNA model occasionally overlapped with predicted cas9 coding regions, emphasizing the importance of expanding our search windows for novel structure RNAs in coding regions. We also demonstrated that the antirepeat sequence in this tracrRNA model can be used to accurately assign thousands of predicted CRISPR arrays to type II-C systems. This study highlights the importance of unbiased identification of candidate structured RNAs across CRISPR-Cas systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Structural modification of fentanyls for their retrospective identification by gas chromatographic analysis using chloroformate chemistry

Abstract The one-step breakdown and derivatization of a panel of nine fentanyls to yield uniquely tagged products that can be detected by Electron Ionization Gas Chromatography-Mass Spectrometry (EI-GC-MS) is presented. The method involves the treatment of the synthetic opioids with 2,2,2-trichloroethoxycarbonyl chloride (TrocCl) at 60 °C for 3 h in dichloromethane and furnishes two products from one fentanyl molecule that can be used to retrospectively identify the original opioid. Parameters that were studied and fully optimized for the method included temperature, solvent, nature of scavenging base and reaction time. One of the two resulting products from the reaction bears the trichloroethoxycarbonyl (Troc) tag attached to the norfentanyl portion of the original opioid and greatly aids in the opioid detection and identification process. The methodology has been applied to the chemical modification of a panel of nine fentanyls and in all cases the molecular ion peak for the Troc-norfentanyl product bearing the distinctive trichloroethyl isotopic signature can be clearly observed. The method’s LLOD was determined to be 10 ng/mL while its LLOQ was found to be 20 ng/mL. This methodology represents the first application of chloroformates in the chemical modification of this class of synthetic opioids that are notoriously inert to common derivatization strategies available for GC–MS analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1991

System identification and control of the JPL active structure

This paper describes recent advances in structural quieting technology as applied to active truss structures intended for high precision space based optics applications. Collocated active damping control loops are designed in order to impedance match piezoelectric active members to the structure. Noncollocated control loops are also studied in relation to controlling lightly damped structures.

Fanson, J. L.↗

NASA NTRS1990

A Hankel singular value approach for identification of low level dynamics in flexible structures

The intensity of dynamics in a flexible structure is characterized by its Hankel singular values. Low level dynamics may be caused by generic properties of a structure or by its actuator and sensor configurations. In the latter case, it is shown that the dynamics can significantly be amplified by small perturbations of actuator and/or sensor configurations. In the presented examples, the variations of sensor configuration of 0.05 or less caused an increase of Hankel singular values of order 1000. This approach is useful for model reduction and model order determination in the presence of noise.

Gawronski, W.↗

DOE OSTI2022

TEM-based phase characterization of $\mathrm{U–19Pu–10Zr}$ irradiated in ATR

We report the results of the microstructural examination of the irradiated U–19Pu–10Zr fuel. New insights gained using selective area electron diffraction analysis in a transmission electron microscope provide crystallographic information on the phases previously identified based primarily on the chemical compositions. After irradiation, the microstructure of the fuel separates into γ-(U, Pu, Zr) in the central region with a secondary nanocrystalline UO 2 phase, γ-(U, Pu, Zr) with a secondary ZrO 2 phase in the intermediate, and ζ-(U, Pu) in the outer regions. While the surface microstructural features and porosity indicate separation into three concentric zones consistent with the existing constituent redistribution model, crystallographically the fuel consists of two zones: inner (with γ-(U, Pu, Zr) as a matrix phase) and outer (with ζ-(U, Pu) as a matrix phase). Our results highlight the importance of crystal structure in phase identification and can be used to supplement the existing constituent redistribution model.

extreme environment↗

DOE OSTI2021

Structural, Electrical, and Electromechanical Properties of Inverse Hybrid Perovskites from First-Principles: The Case of (CH 3 NH 3 ) 3 OI

Inverse-hybrid perovskites (IHPs) with large polarization have recently been predicted from first-principles computations. Here, we use one representative from the IHP class of materials, (CH 3 NH 3 ) 3 OI (MA3OI), to propose a route to the first-principles prediction of structural and electrical properties, such as polarization, polarization reversibility, and the associated coercive field for hybrid organic–inorganic perovskites. The route relies on the construction of the polarization reversal path that models experimental measurements. Such a path was found to play an important role in the ground-state search as well as in the identification of competing structural variations. The latter is believed to be the origin of the structural disorder that is characteristic of hybrid organic–inorganic perovskites. The application of such an approach to MA3OI leads to the prediction of several structural variations that are expected to result in a structurally disordered phase above 766 K and of the polar ground state with a polarization of 25.3 μC/cm 2 that is reversible with the application of an electric field. The upper estimate for the coercive field associated with homogeneous polarization reversal is 6.9 GV/m. The piezoelectric constants of MA3OI are predicted to be an order of magnitude smaller in comparison with a prototypical inorganic ferroelectric PbTiO 3 ; however, the low symmetry of the MA3OI structure yields finite values for all components of the piezoelectric tensor. The polarization in MA3OI is tunable by the epitaxial strain (11.5% change under 5% epitaxial strain), although less so as compared with PbTiO 3 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1988

Parameter identification of material constants in a composite shell structure

One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem.

Martinez, David R.↗

DOE OSTI2024

Structure Sensitive Reaction Kinetics of Chiral Molecules on Intrinsically Chiral Surfaces

Enantiospecific heterogeneous catalysis utilizes chiral surfaces to resolve enantiomers via structure sensitive surface chemistry. The catalyst design challenge is the identification of chiral surface structures that maximize enantiospecificity. Herein, we develop data driven models for the enantiospecificity of tartaric acid reactions on chiral Cu(hkl) R&S surfaces. Measurements of enantiospecific rate constants were obtained by using curved Cu(hkl) R&S surfaces that enable kinetic measurements on hundreds of chiral surface orientations. One model uses feature vectors derived from generalized coordination numbers to capture the local structure around Cu atoms exposed by the Cu(hkl) R&S surfaces. The second model introduces the use of chiral cubic harmonic functions to capture the symmetry constraints of the face-centered cubic Cu structure. The model using 58 generalized coordination numbers has a fitting error similar to that of the model using only 5 cubic harmonic functions. The two models predict maxima in the enantiospecificity on surfaces with very similar surface orientations. The models developed in this work are applicable for any enantiospecific reaction happening on any chiral material with a cubic lattice structure, opening the way to understanding the surface structure sensitivity of the enantiospecific reaction kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Vibrational modes and crystallographic structure of Cd 3 As 2 and (Cd 1-x Zn x ) 3 As 2 epilayers

Low-temperature Raman scattering is used to study the crystal structure of molecular-beam epitaxially grown layers of the Dirac semimetal Cd 3 As 2 and its related alloy (Cd 1-x Zn x ) 3 As 2 . The combination of narrow-linewidth spectra, multiple growth directions and full polarization analysis allows improved accuracy in identifying the irreducible representation of over 57 Raman-active vibrations. Several disagreements with previous identifications are found. Structurally, the results agree with the centrosymmetric I41/acd space group of bulk-grown Cd 3 As 2 and are clearly distinct from the Raman spectra of nanoscale platelets and wires. Three-fold twinning is seen in (112) Cd 3 As 2 grown on (111) zincblende substrates corresponding to the three possible tetragonal orientations. In dilute (Cd 1-x Zn x ) 3 As 2 , phonons have a frequency and scattering amplitude dependence on Zn concentration that is continuous with Cd 3 As 2 but at least one frequency is absent at the alloy endpoint, preventing a simple one-mode description of the alloy phonon.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Imaging gate-tunable Tomonaga–Luttinger liquids in 1H-MoSe 2 mirror twin boundaries

One-dimensional electron systems exhibit fundamentally different properties than higher-dimensional systems. For example, electron-electron interactions in one-dimensional electron systems have been predicted to induce Tomonaga-Luttinger liquid behaviour. Naturally occurring grain boundaries in single-layer transition metal dichalcogenides exhibit one-dimensional conducting channels that have been proposed to host Tomonaga-Luttinger liquids, but charge density wave physics has also been suggested to explain their behaviour. Clear identification of the electronic ground state of this system has been hampered by an inability to electrostatically gate such boundaries and tune their charge carrier concentration. Here we present a scanning tunnelling microscopy and spectroscopy study of gate-tunable mirror twin boundaries in single-layer 1H-MoSe 2 devices. Gating enables scanning tunnelling microscopy and spectroscopy for different mirror twin boundary electron densities, thus allowing precise characterization of electron-electron interaction effects. Visualization of the resulting mirror twin boundary electronic structure allows unambiguous identification of collective density wave excitations having two velocities, in quantitative agreement with the spin-charge separation predicted by finite-length Tomonaga-Luttinger liquid theory.

36 MATERIALS SCIENCE↗

NASA NTRS1987

Recent advances in structural dynamics of large space structures

Recent progress in the area of structural dynamics of large space structures is reviewed. Topics include system identification, large angle slewing of flexible structures, definition of scaling limitations in structural models, and recent results on a tension-stabilized antenna concept known as the hoop-column. Increasingly complex laboratory experiments guide most of the activities leading to realistic technological developments. Theoretical progress in system identification based on system realization theory resulting in unification of several methods is reviewed. Experimental results from implementation of a theoretical large-angle slewing control approach are shown. Status and results of the development of a research computer program for analysis of the transient dynamics of large angle motion of flexible structures are presented. Correlation of results from analysis and vibration tests of the hoop-column antenna concepts are summarized.

Pinson, Larry D.↗

NASA NTRS1987

Recent advances in structural dynamics of large space structures

Pinson, Larry D.↗

DOE OSTI2021

A series of Rb 4 Ln 2 (P 2 S 6 )(PS 4 ) 2 (Ln = La, Ce, Pr, Nd, Sm, Gd) rare earth thiophosphates with two distinct thiophosphate units [P V S 4 ] 3- and [P IV 2 S 6 ] 4-

A series of rubidium rare earth thiophosphates with the formula Rb 4 Ln 2 (P 2 S 6 )(PS 4 ) 2 (Ln = La, Ce, Pr, Nd, Sm, and Gd) were synthesized using the high temperature molten flux crystal growth method utilizing a RbBr flux. Single crystals of all title compounds, as well as phase pure powders of the La-, Ce-, and Sm-containing compositions, were obtained. Single crystals of the title compounds were characterized by single crystal and powder X-ray diffraction for structure and phase identification. Rb 4 Ln 2 (P 2 S 6 )(PS 4 ) 2 crystallizes in the monoclinic crystal system adopting the P2 1 /n space group for the large rare earths (Ln = La, Ce, Pr) and the C2/c space group for the smaller rare earths (Ln = Nd, Sm, Gd). This Rb 4 Ln 2 (P 2 S 6 )(PS 4 ) 2 series is a rare example of thiophosphates containing both tetrahedral [P V S 4 ] 3– and dimeric [P IV 2 S 6 ] 4– thiophosphate units that, in this structural family, link corrugated rare earth sulfide chains into sheets. Here, the band gaps of the materials were determined from UV–Vis data and the fluorescence spectrum of Rb 4 Ce 2 (P 2 S 6 )(PS 4 ) 2 was collected. Optical band gaps were estimated to be 2.9 and 2.4 for the Nd and Sm analogues, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Fault Detection on Seismic Structural Images Using a Nested Residual U-Net

Automatic identification of faults on seismic structural images is a challenging yet crucial task in quantitative seismic interpretation. Human picking or attribute-based fault detection methods may misidentify faults on noisy, complex seismic images. In this work, we develop a new automatic fault detection method using a nested residual U-shaped convolutional neural network. Each of the encoders and decoders in this neural network is a residual U-Net, leading to a nested architecture. The final fault map results from the fusion of three fault maps with low, medium, and high fault resolutions. We demonstrate the excellent fault-detection capability of our nested neural network using a series of synthetic and field seismic images. We find that our approach produces clearer and more interpretable fault maps than the current state-of-the-art U-Net fault detection method, particularly on noisy seismic images. Our new automatic fault detection method can facilitate reliable quantitative seismic interpretation on field seismic images.

58 GEOSCIENCES↗

NASA NTRS1994

High Fidelity Modeling of Evolutionary Structures in IMOS

A methodology is proposed for testing, modal identification, and model correlation of structures which are assembled in an evolutionary manner. The methodology prescribes initial testing of a base structure without any attached components. The experimental modal properties are used to update the physical properties of the base structure finite element model using a Bayesian Estimation Technique (BET). The BET is implemented in METLAB using IMOS functions. As components are added to the base structure, additional tests are performed. Three testing options are proposed, all of which enable estimation of the physical parameters of the components alone. Furthermore, improvements to the original BET implementation have been made, which contribute to higher fidelity models and more efficient computational times.

structures testing assembling modeling BET Bayesia↗

DOE OSTI2023

Spatially confined protein assembly in hierarchical mesoporous metal-organic framework

Immobilization of biomolecules into porous materials could lead to significantly enhanced performance in terms of stability towards harsh reaction conditions and easier separation for their reuse. Metal-Organic Frameworks (MOFs), offering unique structural features, have emerged as a promising platform for immobilizing large biomolecules. Although many indirect methods have been used to investigate the immobilized biomolecules for diverse applications, understanding their spatial arrangement in the pores of MOFs is still preliminary due to the difficulties in directly monitoring their conformations. To gain insights into the spatial arrangement of biomolecules within the nanopores. We used in situ small-angle neutron scattering (SANS) to probe deuterated green fluorescent protein (d-GFP) entrapped in a mesoporous MOF. Our work revealed that GFP molecules are spatially arranged in adjacent nanosized cavities of MOF-919 to form “assembly” through adsorbate-adsorbate interactions across pore apertures. Our findings, therefore, lay a crucial foundation for the identification of proteins structural basics under confinement environment of MOFs.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

On identified predictive control

Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

Bialasiewicz, Jan T.↗

DOE OSTI2020

Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets

Thousands of chemical properties can be calculated for small molecules, which can be used to place the molecules within the context of a broader “chemical space.” These definitions vary based on compounds of interest and the goals for the given chemical space definition. Here, we introduce a customizable (i.e., modular) Python module, chespa, built to easily assess different chemical space definitions through cluster-ing of compounds in these spaces and visualize trends of these clusters. To demonstrate this, chespa currently streamlines prediction of vari-ous molecule descriptors (predicted chemical properties, molecular substructures, AI-based chemical space, and chemical class ontology) in order to test 6 different chemical space definitions. Furthermore, we investigated how these varying definitions trend with mass spectrometry (MS)-based observability, i.e., the ability of a molecule to be observed with MS (e.g., as a function of the molecule ionizability), using an example data set from the U.S. EPA's Non-Targeted Analysis Collaborative Trial (ENTACT), where blinded samples had been analyzed previously, providing 1,398 data points. Improved understanding of observability would offer many advantages in small molecule identifica-tion, such as (i) a priori selection of experimental conditions based on suspected sample composition, (ii) the ability to reduce the number of candidate structures during compound identification by removing those less likely to ionize, and, in turn, (iii) a reduced false discovery rate and increased confidence in identifications. Factors controlling observability are not fully understood, making prediction of this property non-trivial and a prime candidate for chemical space analysis. Chespa is available at github.com/pnnl/chespa.

Nunez, Jamie↗