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Results for “structural complexity”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Residual stress distribution in an additively manufactured complex structure by neutron diffraction measurement

Residual stress in an aerodynamically shaped Ni-based superalloy airfoil fabricated by laser powder bed fusion was measured by neutron diffraction. The experiment was conducted by considering the complex shape, implementing computer aided experiment planning, and automatic alignment at each rapid measurement. The 3-dimensional (3D) residual stress distribution in the airfoil is presented in this work, which lacks symmetry due to the complex geometry of the airfoil. In conclusion, the results provide theoretical thermal processing models a complete residual stress dataset of simulation validation on 3D shape complex structure.

Residual stress↗
DOE OSTI2016

Predicting biomass of hyperdiverse and structurally complex central Amazonian forests - a virtual approach using extensive field data

Notice on corrigendum: This paper has a corresponding corrigendum published. Please read the corrigendum first. Old-growth forests are subject to substantial changes in structure and species composition due to the intensification of human activities, gradual climate change and extreme weather events. Trees store ca. 90 % of the total aboveground biomass (AGB) in tropical forests and precise tree biomass estimation models are crucial for management and conservation. In the central Amazon, predicting AGB at large spatial scales is a challenging task due to the heterogeneity of successional stages, high tree species diversity and inherent variations in tree allometry and architecture. We parameterized generic AGB estimation models applicable across species and a wide range of structural and compositional variation related to species sorting into height layers as well as frequent natural disturbances. We used 727 trees (diameter at breast height ≥ 5 cm) from 101 genera and at least 135 species harvested in a contiguous forest near Manaus, Brazil. Sampling from this data set we assembled six scenarios designed to span existing gradients in floristic composition and size distribution in order to select models that best predict AGB at the landscape level across successional gradients. We found that good individual tree model fits do not necessarily translate into reliable predictions of AGB at the landscape level. When predicting AGB (dry mass) over scenarios using our different models and an available pantropical model, we observed systematic biases ranging from -31 % (pantropical) to +39 %, with root-mean-square error (RMSE) values of up to 130 Mg ha -1 (pantropical). Our first and second best models had both low mean biases (0.8 and 3.9 %, respectively) and RMSE (9.4 and 18.6 Mg ha -1 ) when applied over scenarios. Predicting biomass correctly at the landscape level in hyperdiverse and structurally complex tropical forests, especially allowing good performance at the margins of data availability for model construction/calibration, requires the inclusion of predictors that express inherent variations in species architecture. The model of interest should comprise the floristic composition and size-distribution variability of the target forest, implying that even generic global or pantropical biomass estimation models can lead to strong biases. Reliable biomass assessments for the Amazon basin (i.e., secondary forests) still depend on the collection of allometric data at the local/regional scale and forest inventories including species-specific attributes, which are often unavailable or estimated imprecisely in most regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design. However, few user-friendly tools leveraging the latest deep learning technology for inter-chain contact prediction and the distance-based modelling to predict protein quaternary structures are available. To address this gap, we develop DeepComplex, a web server for predicting structures of dimeric protein complexes. It uses deep learning to predict inter-chain contacts in a homodimer or heterodimer. The predicted contacts are then used to construct a quaternary structure of the dimer by the distance-based modelling, which can be interactively viewed and analysed. The web server is freely accessible and requires no registration. It can be easily used by providing a job name and an email address along with the tertiary structure for one chain of a homodimer or two chains of a heterodimer. The output webpage provides the multiple sequence alignment, predicted inter-chain residue-residue contact map, and predicted quaternary structure of the dimer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Block-induced Complex Structures Building the Flare-productive Solar Active Region 12673

Solar active region (AR) 12673 produced 4 X-class, 27 M-class, and numerous lower-class flares during its passage across the visible solar disk in 2017 September. Our study is to answer the questions why this AR was so flare-productive and how the X9.3 flare, the largest one of the past decade, took place. We find that there was a sunspot in the initial several days, and then two bipolar regions emerged nearby it successively. Due to the standing of the pre-existing sunspot, the movement of the bipoles was blocked, while the pre-existing sunspot maintained its quasi-circular shaped umbra only with the disappearance of a part of penumbra. Thus, the bipolar patches were significantly distorted, and the opposite polarities formed two semi-circular shaped structures. After that, two sequences of new bipolar regions emerged within the narrow semi-circular zone, and the bipolar patches separated along the curved channel. The new bipoles sheared and interacted with the previous ones, forming a complex topological system, during which numerous flares occurred. At the highly sheared region, a great deal of free energy was accumulated. On September 6, one negative patch near the polarity inversion line began to rapidly rotate and shear with the surrounding positive fields, and consequently the X9.3 flare erupted. Our results reveal that the block-induced complex structures built the flare-productive AR and the X9.3 flare was triggered by an erupting filament due to the kink instability. To better illustrate this process, a block-induced eruption model is proposed for the first time.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly, this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Analysis and Implications of Structural Complexity in Low Lattice Thermal Conductivity High Thermoelectric Performance PbTe–PbSnS 2 Composites

The high-performance PbTe-SnTe-PbS-thermoelectric system forms a completely new composite PbTe PbSnS2 with high n-type figure of merit. Electron diffraction and high-resolution electron microscopy characterization of the thermoelectric composite PbTe + 25% PbSnS2 reveals that the system is nanostructured, with PbSnS(2)nanocrystals in the range Of 80 to 500 nm in size. In most of the cases, they are endotaxially grown within the PbTe matrix. Three independent crystal superstructures were observed for the PbSnS2 inclusions, originating from the same parent SnS-type structure. The presence of the parent structure is not excluded. Modified structural models for two of the superstructures observed in the PbSnS2 precipitates are proposed: Often, more than one of the structural phases am observed In the same nanocrystal, providing one extra phonon scattering factor in the system. Evidence was also found for the growth process of the nanocrystals, starting from PbS and followed by gradual dissolving of SnS. Our findings suggest that this nanostructured thermoelectric composite exhibits unique structural complexity, which Contributes to the low lattice thermal :conductivity reported for these nanocomposite materials.

Ioannidou, Chrysoula↗
DOE OSTI2020

Forest Structural Complexity and Biomass Predict First-Year Carbon Cycling Responses to Disturbance

The pre-disturbance vegetation characteristics that predict carbon (C) cycling responses to disturbance are not well known. To address this gap, we initiated the Forest Resilience Threshold Experiment, a manipulative study in which more than 3600 trees were stem girdled to achieve replicated factorial combinations of four levels (control, 45, 65, and 85% gross defoliation) of disturbance severity and two disturbance types (targeting upper or lower canopy strata). Applying a standardized stability framework in which initial C cycling resistance to disturbance was calculated as the first-year natural log response ratio of disturbance and control treatments, we investigated to what extent pre-disturbance levels of species diversity, aboveground woody biomass, leaf area index, and canopy rugosity—a measure of structural complexity—predict the initial responses of subcanopy light-saturated leaf CO 2 assimilation (A sat ), aboveground wood NPP (ANPP w ), and soil respiration (R s ) to phloem-disrupting disturbance. In the year following stem girdling, we found that above-ground C cycling processes, A sat and ANPP w , were highly resistant to increases in disturbance severity, while Rs resistance declined as severity increased. Disturbance type had no effect on first-year resistance. Pre-disturbance aboveground woody biomass, and canopy rugosity were positive predictors of ANPP w resistance and, conversely, negatively related to R s resistance. Subcanopy A sat resistance was not related to pre-disturbance vegetation characteristics. Stability of C uptake processes along with R s declines suggest the net C sink was sustained in the initial months following disturbance. Therefore, we conclude that biomass and complexity are significant, but not universal, predictors of initial C cycling resistance to disturbance. Moreover, our findings highlight the utility of standardized stability measures when comparing functional responses to disturbance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Particle re-acceleration and Faraday-complex structures in the RXC J1314.4-2515 galaxy cluster

Radio relics are sites of electron (re)acceleration in merging galaxy clusters but the mechanism of acceleration and the topology of the magnetic field in and near relics are yet to be understood. We are carrying out an observational campaign on double relic galaxy clusters starting with RXC J1314.4–2515. With Jansky Very Large Array multiconfiguration observations in the frequency range 1–4 GHz, we perform both spectral and polarization analyses, using the rotation measure (RM) synthesis technique. We use archival XMM–Newton observations to constrain the properties of the shocked region. We discover a possible connection between the activity of a radio galaxy and the emission of the eastern radio relic. In the northern elongated arc of the western radio relic, we detect polarized emission with an average polarization fraction of 31 % at 3 GHz and we derive the Mach number of the underlying X-ray shock. Our observations reveal low levels of fractional polarization and Faraday-complex structures in the southern region of the relic, which point to the presence of thermal gas and filamentary magnetic field morphology inside the radio emitting volume. We measured largely different RM dispersion from the two relics. Finally, we use cosmological magnetohydrodynamical simulations to constrain the magnetic field, viewing angle, and to derive the acceleration efficiency of the shock. We find that the polarization properties of RXC J1314.4–2515 are consistent with a radio relic observed at 70° with respect to the line of sight and that the efficient re-acceleration of fossil electrons has taken place.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

GlcNAc-1-P-transferase–tunicamycin complex structure reveals basis for inhibition of N-glycosylation

N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. In conclusion, structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. Here, we demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Synthesis, crystal and electronic structure of the Zintl phase Ba 16 Sb 11 . A case study uncovering greater structural complexity via monoclinic distortion of the tetragonal Ca 16 Sb 11 structure type

The binary Zintl phase Ba 16 Sb 11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba 16 Sb 11 appears to crystallize in the tetragonal Ca 16 Sb 11 structure type (space group $P\bar{4}2_1$m with a=13.5647(9) Å, c=12.4124(12)Å, Z=2, R 1 = 3.14%; wR 2 = 4.77%), there exists an extensive structural disorder. Some Ba 16 Sb 11 crystals were found to be monoclinic and the structure was solved and refined in space group P2 1 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R 1 =5.84 %; wR 2 =9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba 32 Sb 22 (=2×Ba 16 Sb 11 ) can be rationalized as (Ba 2+ ) 32 (Sb 3– ) 20 [Sb 2 ] 4– . Notably, the partitioning of the valence electrons is done taking into an account the homoatomic Sb–Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba 16 Sb 11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.

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

Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools

The rapid development of computational approaches for predicting the structures of T cell receptors (TCRs) and TCR-peptide-major histocompatibility (TCR-pMHC) complexes, accelerated by AI breakthroughs such as AlphaFold, has made it feasible to calculate these structures with increasing accuracy. Although these tools show great potential, their relative accuracy and limitations remain unclear due to the lack of standardized benchmarks. Here, we systematically evaluate seven tools for predicting isolated TCR structures together with six tools for predicting TCR-pMHC complex structures. The methods include homology-based approaches, general prediction tools using AlphaFold, TCR-specific tools derived from AlphaFold2, and the newly developed tFold-TCR model. The evaluation uses a post-training data set comprising 40 αβ TCRs and 27 TCR-pMHC complexes (21 Class I and 6 Class II). Model accuracy is assessed at global, local, and interface levels using a variety of metrics. We find that each tool offers distinct advantages in various aspects of its predictions. AlphaFold2, AlphaFold3, and tFold-TCR excel in overall accuracy of TCR structure prediction, and TCRmodel2 and AlphaFold2 perform well in overall accuracy of TCR-pMHC structure prediction. However, TCR-specific tools derived from AlphaFold2 show lower accuracy in the framework region than both homology-based methods and general-purpose tools such as AlphaFold, and challenges remain for all in modeling CDR3 loops, docking orientations, TCR-peptide interfaces, and Class II MHC-peptide interfaces. Furthermore, these findings will guide researchers in selecting appropriate tools, emphasize the importance of using multiple evaluation metrics to assess model performance, and offer suggestions for improving TCR and TCR-pMHC structure prediction tools.

Chemical structure↗
DOE OSTI2020

NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance

Axon pathfinding is critical for nervous system development, and it is orchestrated by molecular cues that activate receptors on the axonal growth cone. Robo family receptors bind Slit guidance cues to mediate axon repulsion. In mammals, the divergent family member Robo3 does not bind Slits, but instead signals axon repulsion from its own ligand, NELL2. Conversely, canonical Robos do not mediate NELL2 signaling. Here, we present the structures of NELL-Robo3 complexes, identifying a mode of ligand engagement for Robos that is orthogonal to Slit binding. We elucidate the structural basis for differential binding between NELL and Robo family members and show that NELL2 repulsive activity is a function of its Robo3 affinity and is enhanced by ligand trimerization. Our results reveal a mechanism of oligomerization-induced Robo activation for axon guidance and shed light on Robo family member ligand binding specificity, conformational variability, divergent modes of signaling, and evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease

Crosstalk between ion channels and small GTPases is critical during homeostasis and disease, but little is known about the structural underpinnings of these interactions. TRPV4 is a polymodal, calcium-permeable cation channel that has emerged as a potential therapeutic target in multiple conditions. Gain-of-function mutations also cause hereditary neuromuscular disease. Here, we present cryo-EM structures of human TRPV4 in complex with RhoA in the ligand-free, antagonist-bound closed, and agonist-bound open states. These structures reveal the mechanism of ligand-dependent TRPV4 gating. Channel activation is associated with rigid-body rotation of the intracellular ankyrin repeat domain, but state-dependent interaction with membrane-anchored RhoA constrains this movement. Notably, many residues at the TRPV4-RhoA interface are mutated in disease and perturbing this interface by introducing mutations into either TRPV4 or RhoA increases TRPV4 channel activity. Together, these results suggest that RhoA serves as an auxiliary subunit for TRPV4, regulating TRPV4-mediated calcium homeostasis and disruption of TRPV4-RhoA interactions can lead to TRPV4-related neuromuscular disease. These insights will help facilitate TRPV4 therapeutics development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Fyn–Saracatinib Complex Structure Reveals an Active State-like Conformation

Fyn is a Src-family tyrosine kinase implicated in synaptic dysfunction and neuroinflammation across multiple neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). Saracatinib (AZD0530) is a potent Src-family inhibitor that has been explored as a repurposed therapeutic; however, its clinical utility is limited by poor kinase selectivity caused by high sequence conservation within Src-family ATP-binding sites. Here, we combine surface plasmon resonance (SPR) and X-ray crystallography to define saracatinib recognition by the Fyn kinase domain (KD). SPR single-cycle kinetics shows that saracatinib binds the isolated Fyn KD and full-length Fyn with low-nanomolar affinity, whereas dasatinib binds with subnanomolar affinity and markedly slower dissociation. We determined the crystal structure of the Fyn KD-saracatinib complex at 2.22 Å resolution. The kinase adopts an active-like conformation with the DFG motif and αC-helix in the ‘in’ state and a conserved β3 αC Lys-Glu salt bridge. Saracatinib occupies the adenine and ribose pockets, and engages the hinge through direct and water-mediated hydrogen bonding while complementing a hydrophobic back pocket by van der Waals contacts. Comparison with reported saracatinib-bound structures of other kinases suggests that the active-state geometry observed for Fyn creates a pocket not observed in inactive-like complexes, providing a structural handle for designing Fyn-selective inhibitors. Comparison with all saracatinib-bound kinase co-structures currently available in the PDB (ALK2 and PKMYT1) indicates a conserved monodentate hinge binding mode but kinase-dependent αC-helix conformations, providing a structural rationale for designing Fyn-selective analogues.

AZD0530↗
DOE OSTI2014

A new Cu–cysteamine complex: structure and optical properties

Here we report the structure and optical properties of a new Cu–cysteamine complex (Cu–Cy) with a formula of Cu3Cl(SR)2 (R ¼ CH2CH2NH2). This Cu–Cy has a different structure from a previous Cu–Cy complex, in which both thio and amine groups from cysteamine bond with copper ions. Single-crystal X-ray diffraction and solid-state nuclear magnetic resonance results show that the oxidation state of copper in Cu3Cl(SR)2 is +1 rather than +2. Further, Cu3Cl(SR)2 has been observed to show intense photoluminescence and X-ray excited luminescence. More interesting is that Cu3Cl(SR)2 particles can produce singlet oxygen under irradiation by light or X-ray. This indicates that Cu3Cl(SR)2 is a new photosensitizer that can be used for deep cancer treatment as X-ray can penetrate soft tissues. All these findings mean that Cu3Cl(SR)2 is a new material with potential applications for lighting, radiation detection and cancer treatment.

Ma, Lun↗