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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Numerical Simulation of the Structure and Mechanical Properties of Silicene Layers on Graphite during the Lithium Ion Motion

The molecular dynamics method is applied to study structural and mechanical effects appearing during the lithium ion motion in a dc electric field along a planar channel formed by perfect silicene sheets and sheets containing vacancy-type defects. Mono-, di-, tri-, and hexavacancies of rather densely and uniformly filled silicene sheets are arranged one above the other on a graphite substrate. The times of Li{sup +} ion passage through silicene channels with various gaps are determined. The construction of Voronoi polyhedra and truncated polyhedrons, whose centers coincide with the moving ion position allowed revealing the structural features inherent to the two-dimensional layered structure. The nature of stresses appearing in silicene sheets most critical to ion motion over the channel is determined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Coupled Geomechanical Modeling to Assess Cap Rock Integrity and Mechanical Fault Stability: Application to Farnsworth Field Unit Project

Abstract The SWP project is located in a mature waterflood undergoing conversion to CO2-WAG operations in the Farnsworth, Texas, USA. Anthropogenic CO2 is sourced from a fertilizer and an ethanol plant. This work utilizes Farnsworth’s full-field, history-matched, compositional hydrodynamic coupled geomechanical model for assessing the impact of stress changes observed through the history matched field life. Production and injection induced stress changes, fault stability and caprock integrity investigations are performed to project the potential for fault reactivation and the loss of caprock integrity under shear failure. A static mechanical earth model (MEM) was constructed for use in transient coupled geomechanical model based on the existing Southwest Regional Partnership (SWP) geological model. The static MEM inherits the stratigraphic and structural features of the geologic model and incorporates additional overburden, underburden, and sideburden formations required to impose mechanical boundary conditions. Mechanical properties were distributed in the 3D MEM through integration of geophysical logs and 3-dimensional seismic elastic inversion properties using a combination of Bayesian and stochastic interpolation methods. These data are further enhanced by lab derived strength and failure criteria for the caprock interval. Additionally, interpreted faults and other geological features were included as part of the static structural framework to fully represent subsurface hydraulic and mechanical systems and appropriately integrate heterogeneity. Two-way coupling of hydrodynamic flow and geomechanical simulations incorporates the Kozeny-Carman relationship for updating permeability and is history matched through primary, secondary (waterflooding) and tertiary (CO2 WAG) recovery periods before performing a twenty year forecast. Two-way simulations are performed to understand the effective stress perturbations imposed by field operations: water injection and the more recent implementation of WAG. Evaluation of Mohr circles with liquid production and field pressure charts as well as slip tendency and distance to failure metrics indicate that neither our faults or cap rock are critically stressed. This paper presents the results of the Farnsworth initial attempts to integrate the seismic driven 3D MEM into coupled hydrodynamic geomechanical history match simulation workflow.

02 PETROLEUM↗
DOE OSTI2021

Natural Systems Data Package for the Active Trenches of the Low-Level Burial Grounds, Hanford Site, Washington

This document summarizes the available information regarding the natural system (vadose zone and saturated zone) at the active trenches of the 200 West Area and 200 East Area Low-Level Burial Grounds (LLBGs). This information is relevant for developing the natural system fate and transport model for the update of the active trenches performance assessment. This document presents a description of the major features, events, and processes of the natural system at the active trenches of the 200 West Area and 200 East Area LLBGs that involves the geologic features or framework, and the vadose zone and groundwater flow and transport system. The description of the geologic features includes the following items: geologic setting, major structural features, major hydrostratigraphic units, and geologic framework. The discussion concerning vadose zone flow and transport at the active trenches of the 200 West Area and 200 East Area LLBGs includes the following topics: vadose zone features, events, and processes relevant to the development of the vadose zone conceptual model; hydrogeologic units and conditions; factors affecting moisture movement; and flow and transport properties of major units. The discussion concerning the groundwater flow and transport system in the vicinity of the active trenches of the 200 West Area and 200 East Area LLBGs includes the following topics: saturated zone features, events, and processes relevant to the saturated zone conceptual model; hydrogeologic units; groundwater flow conditions; and flow and transport properties.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1973

Evaluation of feasibility of mapping seismically active faults in Alaska

The author has identified the following significant results. ERTS-1 imagery is proving to be exceptionally useful in delineating structural features in Alaska which have never been recognized on the ground. Previously unmapped features such as seismically active faults and major structural lineaments are especially evident. Among the more significant results of this investigation is the discovery of an active strand of the Denali fault. The new fault has a history of scattered activity and was the scene of a magnitude 4.8 earthquake on October 1, 1972. Of greater significance is the disclosure of a large scale conjugate fracture system north of the Alaska Range. This fracture system appears to result from compressive stress radiating outward from around Mt. McKinley. One member of the system was the scene of a magnitude 6.5 earthquake in 1968. The potential value of ERTS-1 imagery to land use planning is reflected in the fact that this earthquake occurred within 10 km of the site which was proposed for the Rampart Dam, and the fault on which it occurred passes very near the proposed site for the bridge and oil pipeline crossing of the Yukon River.

Gedney, L. D.↗
NASA NTRS1973

Some aspects of active tectonism in Alaska as seen on ERTS-1

ERTS-1 imagery is proving to be exceptionally useful in delineating structural features in Alaska which have never been recognized on the ground. Previously unmapped features such as seismically active faults and major structural lineaments are especially evident. Among the more significant results of this investigation is the discovery of an active strand of the Denali fault. The new fault has a history of scattered seismicity and was the scene of a magnitude 4.8 earthquake on October 1, 1972. Perhaps of greater significance is the disclosure of a large scale conjugate fracture system north of the Alaska Range. This fracture system appears to result from compressive stress radiating outward from around the outside of the great bend of the Alaska Range at Mt. McKinley.

Gedney, L. D.↗
DOE OSTI2018

Elucidating a role for the cytoplasmic domain in the Mycobacterium tuberculosis mechanosensitive channel of large conductance

Microbial survival in dynamic environments requires the ability to successfully respond to abrupt changes in osmolarity. The mechanosensitive channel of large conductance (MscL) is a ubiquitous channel that facilitates the survival of bacteria and archaea under severe osmotic down-shock conditions by relieving excess turgor pressure in response to increased membrane tension. A prominent structural feature of MscL, the cytoplasmic C-terminal domain, has been suggested to influence channel assembly and function. In this report, we describe the X-ray crystal structure and electrophysiological properties of a C-terminal domain truncation of the Mycobacterium tuberculosis MscL (MtMscLΔC). A crystal structure of MtMscLΔC solubilized in the detergent n-dodecyl-β-D-maltopyranoside reveals the pentameric, closed state-like architecture for the membrane spanning region observed in the previously solved full-length MtMscL. Electrophysiological characterization demonstrates that MtMscLΔC retains mechano-sensitivity, but with conductance and tension sensitivity more closely resembling full length EcMscL than MtMscL. This study establishes that the C-terminal domain of MtMscL is not required for oligomerization of the full-length channel, but rather influences the tension sensitivity and conductance properties of the channel. The collective picture that emerges from these data is that each MscL channel structure has characteristic features, highlighting the importance of studying multiple homologs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei

The quaternary structure of the redox protein thioredoxin (Trx) has been debated. For bacterial Trx, there is no question regarding its monomeric state. In humans and other eukaryotes, the presence of a cysteine residue at the crystallographic symmetry axis points to the relevance of dimer formation in solution and in vivo . Crystallographic data for shrimp thioredoxin ( Lv Trx) obtained under different redox conditions reveal a dimeric arrangement mediated by a disulfide bond through residue Cys73 and other hydrophobic interactions located in the crystallographic interface, as reported for human Trx. Through the analysis of five mutants located at the crystallographic interface, this study provides structural and biochemical evidence for the existence in solution of monomeric and dimeric populations of wild-type Lv Trx and five mutants. Based on the results of biochemical assays, SAXS studies and the crystallographic structures of three of the studied mutants (Cys73Ser, Asp60Ser and Trp31Ala), it is clear that the Cys73 residue is essential for dimerization. However, its mutation to Ser produces an enzyme which has similar redox activity in vitro to the wild type. A putative regulatory function of dimerization is proposed based on structural analysis. Nonetheless, the biological role of Lv Trx dimerization needs to be experimentally unveiled. Additionally, the findings of this work reopen the discussion regarding the existence of similar behaviour in human thioredoxin, which shares a Cys at position 73 with Lv Trx, a structural feature that is also present in some Trxs from vertebrates and crustaceans.

Campos-Acevedo, Adam A.↗
DOE OSTI2020

TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs

Abstract T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Pressure‐Suppressed Carrier Trapping Leads to Enhanced Emission in Two‐Dimensional Perovskite (HA) 2 (GA)Pb 2 I 7

Abstract A remarkable PL enhancement by 12 fold is achieved using pressure to modulate the structure of a recently developed 2D perovskite (HA) 2 (GA)Pb 2 I 7 (HA= n ‐hexylammonium, GA=guanidinium). This structure features a previously unattainable, extremely large cage. In situ structural, spectroscopic, and theoretical analyses reveal that lattice compression under a mild pressure within 1.6 GPa considerably suppresses the carrier trapping, leading to significantly enhanced emission. Further pressurization induces a non‐luminescent amorphous yellow phase, which is retained and exhibits a continuously increasing band gap during decompression. When the pressure is released to 1.5 GPa, emission can be triggered by above‐band gap laser irradiation, accompanied by a color change from yellow to orange. The obtained orange phase could be retained at ambient conditions and exhibits two‐fold higher PL emission compared with the pristine (HA) 2 (GA)Pb 2 I 7 .

Guo, Songhao↗
DOE OSTI2016

Structural and Rotational Dynamics of Carbon Dioxide in 1-Alkyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquids: The Effect of Chain Length

Ionic liquids (ILs) have been proposed as possible carbon dioxide (CO 2 ) carbon capture media, and so it is useful to understand the dynamics of both the dissolved gas and its IL environment as well as how altering the IL affects these dynamics. With increasing alkyl chain length, it is well established that ILs obtain a mesoscopic structural feature assigned to polarapolar segregation, and the change in structure with chain length affects dynamics. In this work, the dynamics of CO 2 in a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids (ILs), where alkyl is ethyl, butyl, hexyl, or decyl, were investigated using ultrafast infrared spectroscopy by measuring the reorientation and spectral diffusion of carbon dioxide in the ILs. It was found that reorientation of the carbon dioxide occurs on 3 timescales, which correspond to 2 different timescales of restricted wobbling-in-a-cone motions and a long time complete diffusive reorientation. The complete reorientation slows with increasing chain length but less than the increases in viscosity of the bulk liquids. Spectral diffusion, measured with 2D IR spectroscopy, is caused by a combination of the liquids’ structural fluctuations and reorientation of the CO 2 . The data were analyzed using recent theory that takes into account both contributions to spectral diffusion and extracts the structural spectral diffusion. Different components of the structural fluctuations have distinct dependences on the alkyl chain length. All of the dynamics are fast compared to the complete orientational randomization of the bulk ILs, as measured with optical heterodyne detected optical Kerr effect measurements. The results indicate a hierarchy of constraint releases in the liquids that give rise to increasingly slower dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Observation of a mixed close-packed structure in superionic water

The study of superionic (SI) water has been a highly active research area since its theoretical prediction. Despite significant experimental and computational efforts, its melting curve and the stability of different oxygen lattices remain debated, impacting our understanding of SI ice’s peculiar transport properties. Experimental results at lower pressures show disagreement, whereas data at higher pressures are scarce due to the extreme challenges of such experiments. In this work, we present ultrafast X-ray diffraction results of water compressed by multiple shocks to pressures up to ~ 180 GPa. At pressures exceeding 150 GPa and temperatures around 2500 K, our diffraction patterns challenge the pure FCC-SI phase model, providing experimental evidence of the mixed close-packed superionic phase predicted by advanced ab initio calculations. At lower pressures, we observe simultaneous signatures of BCC and FCC structures within a pressure-temperature range consistent with some static-compression experiments, helping to resolve contradictory results in literature. These insights offer new constraints on the stability domains of SI phases and reveal detailed structural features, such as stacking faults. Our results advance the structural understanding of high-pressure SI ice to a level approaching that of ice I polymorphs, with potential implications for water-rich interiors of giant planets.

Andriambariarijaona, Leon [Centre National de la R↗
DOE OSTI2016

Measurement and modeling of short and medium range order in amorphous Ta 2 O 5 thin films

Here, amorphous films and coatings are rapidly growing in importance. Yet, there is a dearth of high-quality structural data on sub-micron films. Not understanding how these materials assemble at atomic scale limits fundamental insights needed to improve their performance. Here, we use grazing-incidence x-ray total scattering measurements to examine the atomic structure of the top 50–100 nm of Ta 2 O 5 films; mirror coatings that show high promise to significantly improve the sensitivity of the next generation of gravitational-wave detectors. Our measurements show noticeable changes well into medium range, not only between crystalline and amorphous, but also between as-deposited, annealed and doped amorphous films. It is a further challenge to quickly translate the structural information into insights into mechanisms of packing and disorder. Here, we illustrate a modeling approach that allows translation of observed structural features to a physically intuitive packing of a primary structural unit based on a kinked Ta-O-Ta backbone. Our modeling illustrates how Ta-O-Ta units link to form longer 1D chains and even 2D ribbons, and how doping and annealing influences formation of 2D order. We also find that all the amorphousTa 2 O 5 films studied in here are not just poorly crystalline but appear to lack true 3D order.

36 MATERIALS SCIENCE↗
DOE OSTI2017

A global view of structure–function relationships in the tautomerase superfamily

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Multi-scale structural analysis of proteins by deep semantic segmentation

Abstract Motivation Recent advances in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidate structures that can lead to native folds or designable structures remains a challenge, since few existing metrics capture high-level structural features such as architectures, folds and conformity to conserved structural motifs. Convolutional Neural Networks (CNNs) have been successfully used in semantic segmentation—a subfield of image classification in which a class label is predicted for every pixel. Here, we apply semantic segmentation to protein structures as a novel strategy for fold identification and structure quality assessment. Results We train a CNN that assigns each residue in a multi-domain protein to one of 38 architecture classes designated by the CATH database. Our model achieves a high per-residue accuracy of 90.8% on the test set (95.0% average per-class accuracy; 87.8% average per-structure accuracy). We demonstrate that individual class probabilities can be used as a metric that indicates the degree to which a randomly generated structure assumes a specific fold, as well as a metric that highlights non-conformative regions of a protein belonging to a known class. These capabilities yield a powerful tool for guiding structural sampling for both structural prediction and design. Availability and implementation The trained classifier network, parser network, and entropy calculation scripts are available for download at https://git.io/fp6bd, with detailed usage instructions provided at the download page. A step-by-step tutorial for setup is provided at https://goo.gl/e8GB2S. All Rosetta commands, RosettaRemodel blueprints, and predictions for all datasets used in the study are available in the Supplementary Information. Supplementary information Supplementary data are available at Bioinformatics online.

Eguchi, Raphael R.↗
DOE OSTI2018

Deep clustering of protein folding simulations

Background: We investigate the problem of clustering biomolecular simulations using deep learning techniques. Since biomolecular simulation datasets are inherently high dimensional, it is often necessary to build low dimensional representations that can be used to extract quantitative insights into the atomistic mechanisms that underlie complex biological processes. Results: We use a convolutional variational autoencoder (CVAE) to learn low dimensional, biophysically relevant latent features from long time-scale protein folding simulations in an unsupervised manner. We demonstrate our approach on three model protein folding systems, namely Fs-peptide (14 μs aggregate sampling), villin head piece (single trajectory of 125 μs) and β- β- α (BBA) protein (223 + 102 μs sampling across two independent trajectories). In these systems, we show that the CVAE latent features learned correspond to distinct conformational substates along the protein folding pathways. The CVAE model predicts, on average, nearly 89% of all contacts within the folding trajectories correctly, while being able to extract folded, unfolded and potentially misfolded states in an unsupervised manner. Further, the CVAE model can be used to learn latent features of protein folding that can be applied to other independent trajectories, making it particularly attractive for identifying intrinsic features that correspond to conformational substates that share similar structural features. Conclusions: Together, we demonstrate that the CVAE model can quantitatively describe complex biophysical processes such as protein folding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Robocrystallographer: automated crystal structure text descriptions and analysis

Our ability to describe crystal structure features is of crucial importance when attempting to understand structure–property relationships in the solid state. Here, the authors introduce robocrystallographer, an open-source toolkit for analyzing crystal structures. This package combines new and existing open-source analysis tools to provide structural information, including the local coordination and polyhedral type, polyhedral connectivity, octahedral tilt angles, component-dimensionality, and molecule-within-crystal and fuzzy prototype identification. Using this information, robocrystallographer can generate text-based descriptions of crystal structures that resemble descriptions written by human crystallographers. The authors use robocrystallographer to investigate the dimensionalities of all compounds in the Materials Project database and highlight its potential in machine learning studies.

36 MATERIALS SCIENCE↗