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At least 1,639 records · Page 91
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors

Boronic acid transition-state analog inhibitors (BATSIs) are partners with β-lactam antibiotics for the treatment of complex bacterial infections. Herein, microbiological, biochemical, and structural findings on four BATSIs with the FOX-4 cephamycinase, a class C β-lactamase that rapidly hydrolyzes cefoxitin, are revealed. FOX-4 is an extended-spectrum class C cephalosporinase that demonstrates conformational flexibility when complexed with certain ligands. Like other β-lactamases of this class, studies on FOX-4 reveal important insights into structure–activity relationships. We show that SM23, a BATSI, shows both remarkable flexibility and affinity, binding similarly to other β-lactamases, yet retaining an IC 50 value < 0.1 μM. Our analyses open up new opportunities for the design of novel transition-state analogs of class C enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

New Platinum Complexes from Salen- and Hydroxy-Substituted Salpn-Naphthalene Ligands with CO 2 Reduction Activity

The electrocatalytic reduction of carbon dioxide (CO 2 ) into added-value products is a promising alternative to completing the cycle of atmospheric CO 2 . We report two new platinum complexes—a salen-like naphthalene (PtL1) and a hydroxy-substituted salpn naphthalene (PtL2)—that are capable of activating CO 2 to produce carbon monoxide (CO). The predominant keto tautomer of the non-innocent ligands was determined using DFT calculations and UV-Vis spectroscopy. The PtL2 complex has a CO Faradaic efficiency >40% in the presence of water as a sacrificial proton source at -2.5 V vs. Fc/Fc + . The addition of the hydroxy group in combination with water as a proton source decreased the reduction potential and increased the CO formation tenfold when compared to PtL1.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2023

Probing Boron Vacancy Complexes in h-BN Semi-Bulk Crystals Synthesized by Hydride Vapor Phase Epitaxy

Hexagonal BN (h-BN) has emerged as an important ultrawide bandgap (UWBG) semiconductor (Eg~6 eV). The crystal growth technologies for producing semi-bulk crystals/epilayers in large wafer sizes and understanding of defect properties lag decades behind conventional III-nitride wide bandgap (WBG) semiconductors. Here we report probing of boron vacancy (VB)-related defects in freestanding h-BN semi-bulk wafers synthesized by hydride vapor phase epitaxy (HVPE). A photocurrent excitation spectroscopy (PES) was designed to monitor the transport of photoexcited holes from deep-level acceptors. A dominant transition line at 1.66 eV with a side band near 1.62 eV has been directly observed, which matches well with the calculated energy levels of 1.65 for the VB-H deep acceptor in h-BN. The identification of VB complexes via PES measurement was further corroborated by the temperature-dependent dark resistivity and secondary ion mass spectrometry measurements. The results presented here suggested that it is necessary to focus on the optimization of V/III ratio during HVPE growth to minimize the generation of VB-related defects and to improve the overall material quality of h-BN semi-bulk crystals. The work also provided a better understanding of how VB complexes behave and affect the electronic and optical properties of h-BN.

36 MATERIALS SCIENCE↗
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 OSTI2024

Evidence of Cooperative Effects for the Fe(phen) 2 (NCS) 2 Spin Crossover Molecular Complex in Polyaniline Plus Iron Magnetite

The spin crossover complex Fe(phen) 2 (NCS) 2 and its composite, Fe(phen) 2 (NCS) 2 , combined with the conducting polymer polyaniline (PANI) plus varying concentrations of iron magnetite (Fe 3 O 4 ) nanoparticles were studied. A cooperative effect is evident from the hysteresis width in the plot of magnetic susceptibility multiplied by temperature versus temperature (χ m T versus T) for Fe(phen) 2 (NCS) 2 with PANI plus varying concentrations of Fe 3 O 4 nanoparticles. The hysteresis width in the composites vary no more than 2 K with respect to the pristine Fe(phen) 2 (NCS) 2 spin crossover crystallites despite the fact that there exists a high degree of miscibility of the Fe(phen) 2 (NCS) 2 spin crossover complex with the PANI. The Fe 3 O 4 nanoparticles in the Fe(phen) 2 (NCS) 2 plus PANI composite tend to agglomerate at higher concentrations regardless of the spin state of Fe(phen) 2 (NCS) 2 . Of note is that the Fe 3 O 4 nanoparticles are shown to be antiferromagnetically coupled with the Fe(phen) 2 (NCS) 2 when Fe(phen) 2 (NCS) 2 is in the high spin state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A P-61 Black Widow Inspired Palladium Biladiene Complex for Efficient Sensitization of Singlet Oxygen Using Visible Light

Photodynamic therapy (PDT) is a promising treatment option that ablates cancerous cells and tumors via photoinduced sensitization of singlet oxygen. Over the last few decades, much work has been devoted to the development of new photochemotherapeutic agents for PDT. A wide variety of macrocyclic tetrapyrrole based photosensitizers have been designed, synthesized and characterized as PDT agents. Many of these complexes have a variety of issues that pose a barrier to their use in humans, including biocompatibility, inherent toxicity, and synthetic hurdles. We have developed a non-traditional, non-cyclic, and non-aromatic tetrapyrrole ligand scaffold, called the biladiene (DMBil1), as an alternative to these traditional photosensitizer complexes. Upon insertion of a heavy atom such as Pd 2+ center, Pd[DMBil1] generates singlet oxygen in substantial yields (Φ Δ = 0.54, λ exc = 500 nm) when irradiated with visible light. To extend the absorption profile for Pd[DMBil1] deeper into the phototherapeutic window, the tetrapyrrole was conjugated with alkynyl phenyl groups at the 2- and 18-positions (Pd[DMBil2-PE]) resulting in a significant redshift while also increasing singlet oxygen generation (Φ Δ = 0.59, 600 nm). To further modify the dialkynyl-biladiene scaffold, we conjugated a 1,8-diethynylanthracene with to the Pd[DMBil1] tetrapyrrole in order to further extend the compound’s π-conjugation in a cyclic loop that spans the entire tetrapyrrole unit. This new compound (Pd[DMBil2-P61]) is structurally reminiscent of the P61 Black Widow aircraft and absorbs light into the phototherapeutic window (600–900 nm). In addition to detailing the solid-state structure and steady-state spectroscopic properties for this new biladiene, photochemical sensitization studies demonstrated that Pd[DMBil2-P61] can sensitize the formation of 1 O 2 with quantum yields of Φ Δ = 0.84 upon irradiation with light λ = 600 nm. These results distinguish the Pd[DMBil2-P61] platform as the most efficient biladiene-based singlet oxygen photosensitizer developed to date. When taken together, the improved absorption in the phototherapeutic window and high singlet oxygen sensitization efficiency of Pd[DMBil2-P61] mark this compound as a promising candidate for future study as an agent of photodynamic cancer therapy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Maize Terpene Synthase 8 (ZmTPS8) Contributes to a Complex Blend of Fungal-Elicited Antibiotics

In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Entry and Disposition of Zika Virus Immune Complexes in a Tissue Culture Model of the Maternal-Fetal Interface

Zika virus (ZIKV) infections have been associated with an increased incidence of severe microcephaly and other neurodevelopmental disorders in newborn babies. Passive immunization with anti-ZIKV neutralizing antibodies has the potential to become a feasible treatment or prophylaxis option during pregnancy. Prior to clinical use, such antibodies should be assessed for their ability to block ZIKV passage to the fetus. We used human placental and mammalian cell monolayers that express FcRn and laboratory preparations of anti-ZIKV antibodies as a model system to investigate the disposition of ZIKV/antibody immune complexes (ICs) at the maternal-fetal interface. We further characterized solution properties of the ICs to evaluate whether these are related to in vitro effects. We found that both ZIKV and ZIKV envelope glycoprotein can enter and passage through epithelial cells, especially those that overexpress FcRn. In the presence of ZIKV antibodies, Zika virus entry was bimodal, with reduced entry at the lowest (0.3–3 ng/mL) and highest (µg/mL) antibody concentrations. Intermediate concentrations attenuated inhibition or enhanced viral entry. With respect to anti-ZIKV antibodies, we found that their degradation was accelerated when presented as ICs containing increased amounts of ZIKV immunogen. Of the two monoclonal antibodies tested, the preparation with higher aggregation also exhibited higher degradation. Our studies confirm that intact Zika virus and its envelope immunogen have the potential to enter and be transferred across placental and other epithelial cells that express FcRn. Presence of anti-ZIKV IgG antibodies can either block or enhance cellular entry, with the antibody concentration playing a complex role in this process. Physicochemical properties of IgG antibodies can influence their degradation in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A Survey for New Stars and Brown Dwarfs in the Ophiuchus Star-forming Complex

We have performed a survey for new members of the Ophiuchus cloud complex using high-precision astrometry from the second data release of Gaia, proper motions measured with multi-epoch images from the Spitzer Space Telescope, and color–magnitude diagrams constructed with photometry from various sources. Through spectroscopy of candidates selected with those data, we have identified 155 new young stars. Based on available measurements of kinematics, we classify 102, 47, and 6 of those stars as members of Ophiuchus, Upper Sco, and other populations in Sco–Cen, respectively. We have also assessed the membership of all other stars in the vicinity of Ophiuchus that have spectroscopic evidence of youth from previous studies, arriving at a catalog of 373 adopted members of the cloud complex. For those adopted members, we have compiled mid-infrared photometry from Spitzer and the Wide-field Infrared Survey Explorer and have used mid-infrared colors to identify and classify circumstellar disks. We find that 210 of the members show evidence of disks, including 48 disks that are in advanced stages of evolution. Finally, we have estimated the relative median ages of the populations near the Ophiuchus clouds and the surrounding Upper Sco association using absolute K-band magnitudes (M {sub K}) based on Gaia parallaxes. If we adopt an age 10 Myr for Upper Sco, then the relative values of M {sub K} imply median ages of ∼2 Myr for L1689 and embedded stars in L1688, 3–4 Myr for low-extinction stars near L1688, and ∼6 Myr for the group containing ρ Oph.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Disk Evolution Study through Imaging of Nearby Young Stars (DESTINYS): A Panchromatic View of DO Tau’s Complex Kilo-astronomical-unit Environment

While protoplanetary disks are often treated as isolated systems in planet formation models, observations increasingly suggest that vigorous interactions between Class II disks and their environments are not rare. DO Tau is a T Tauri star that has previously been hypothesized to have undergone a close encounter with the HV Tau system. As part of the DESTINYS ESO Large Programme, we present new Very Large Telescope (VLT)/SPHERE polarimetric observations of DO Tau and combine them with archival Hubble Space Telescope (HST) scattered-light images and Atacama Large Millimeter/submillimeter Array (ALMA) observations of CO isotopologues and CS to map a network of complex structures. The SPHERE and ALMA observations show that the circumstellar disk is connected to arms extending out to several hundred astronomical units. HST and ALMA also reveal stream-like structures northeast of DO Tau, some of which are at least several thousand astronomical units long. These streams appear not to be gravitationally bound to DO Tau, and comparisons with previous Herschel far-IR observations suggest that the streams are part of a bridge-like structure connecting DO Tau and HV Tau. We also detect a fainter redshifted counterpart to a previously known blueshifted CO outflow. While some of DO Tau's complex structures could be attributed to a recent disk–disk encounter, they might be explained alternatively by interactions with remnant material from the star formation process. These panchromatic observations of DO Tau highlight the need to contextualize the evolution of Class II disks by examining processes occurring over a wide range of size scales.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Holographic pseudoentanglement and the complexity of the AdS/CFT dictionary

The `quantum gravity in the lab' paradigm suggests that quantum computers might shed light on quantum gravity by simulating the CFT side of the AdS/CFT correspondence and mapping the results to the AdS side. This relies on the assumption that the duality map (the `dictionary') is efficient to compute. In this work, we show that the complexity of the AdS/CFT dictionary is surprisingly subtle: there might be cases in which one can efficiently apply operators to the CFT state (a task we call 'operator reconstruction') without being able to extract basic properties of the dual bulk state such as its geometry (which we call 'geometry reconstruction'). Geometry reconstruction corresponds to the setting where we want to extract properties of a completely unknown bulk dual from a simulated CFT boundary state. We demonstrate that geometry reconstruction may be generically hard due to the connection between geometry and entanglement in holography. In particular we construct ensembles of states whose entanglement approximately obey the Ryu-Takayanagi formula for arbitrary geometries, but which are nevertheless computationally indistinguishable. This suggests that even for states with the special entanglement structure of holographic CFT states, geometry reconstruction might be hard. This result should be compared with existing evidence that operator reconstruction is generically easy in AdS/CFT. A useful analogy for the difference between these two tasks is quantum fully homomorphic encryption (FHE): this encrypts quantum states in such a way that no efficient adversary can learn properties of the state, but operators can be applied efficiently to the encrypted state. We show that quantum FHE can separate the complexity of geometry reconstruction vs operator reconstruction, which raises the question whether FHE could be a useful lens through which to view AdS/CFT.

FOS: Physical sciences↗
DOE OSTI2026

Domain Knowledge Guided Bayesian Optimization For Autonomous Alignment Of Complex Scientific Instruments

Bayesian Optimization (BO) is a powerful tool for optimizing complex non-linear systems. However, its performance degrades in high-dimensional problems with tightly coupled parameters and highly asymmetric objective landscapes, where rewards are sparse. In such needle-in-a-haystack scenarios, even advanced methods like trust-region BO (TurBO) often lead to unsatisfactory results. We propose a domain knowledge guided Bayesian Optimization approach, which leverages physical insight to fundamentally simplify the search problem by transforming coordinates to decouple input features and align the active subspaces with the primary search axes. We demonstrate this approach's efficacy on a challenging 12-dimensional, 6-crystal Split-and-Delay optical system, where conventional approaches, including standard BO, TuRBO and multi-objective BO, consistently led to unsatisfactory results. When combined with an reverse annealing exploration strategy, this approach reliably converges to the global optimum. The coordinate transformation itself is the key to this success, significantly accelerating the search by aligning input co-ordinate axes with the problem's active subspaces. As increasingly complex scientific instruments, from large telescopes to new spectrometers at X-ray Free Electron Lasers are deployed, the demand for robust high-dimensional optimization grows. Our results demonstrate a generalizable paradigm: leveraging physical insight to transform high-dimensional, coupled optimization problems into simpler representations can enable rapid and robust automated tuning for consistent high performance while still retaining current optimization algorithms.

FOS: Computer and information sciences↗
DOE OSTI2023

Evaluation of global teleconnections in CMIP6 climate projections using complex networks

In climatological research, the evaluation of climate models is one of the central research subjects. As an expression of large-scale dynamical processes, global teleconnections play a major role in interannual to decadal climate variability. Their realistic representation is an indispensable requirement for the simulation of climate change, both natural and anthropogenic. Therefore, the evaluation of global teleconnections is of utmost importance when assessing the physical plausibility of climate projections. We present an application of the graph-theoretical analysis tool δ-MAPS, which constructs complex networks on the basis of spatio-temporal gridded data sets, here sea surface temperature and geopotential height at 500 hPa. Complex networks complement more traditional methods in the analysis of climate variability, like the classification of circulation regimes or empirical orthogonal functions, assuming a new non-linear perspective. While doing so, a number of technical tools and metrics, borrowed from different fields of data science, are implemented into the δ-MAPS framework in order to overcome specific challenges posed by our target problem. Those are trend empirical orthogonal functions (EOFs), distance correlation and distance multicorrelation, and the structural similarity index. δ-MAPS is a two-stage algorithm. In the first place, it assembles grid cells with highly coherent temporal evolution into so-called domains. In a second step, the teleconnections between the domains are inferred by means of the non-linear distance correlation. We construct 2 unipartite and 1 bipartite network for 22 historical CMIP6 climate projections and 2 century-long coupled reanalyses (CERA-20C and 20CRv3). Potential non-stationarity is taken into account by the use of moving time windows. The networks derived from projection data are compared to those from reanalyses. Our results indicate that no single climate projection outperforms all others in every aspect of the evaluation. But there are indeed models which tend to perform better/worse in many aspects. Differences in model performance are generally low within the geopotential height unipartite networks but higher in sea surface temperature and most pronounced in the bipartite network representing the interaction between ocean and atmosphere.

58 GEOSCIENCES↗
DOE OSTI2024

Hector V3.2.0: functionality and performance of a reduced-complexity climate model

Abstract. Hector is an open-source reduced-complexity climate–carbon cycle model that models critical Earth system processes on a global and annual basis. Here, we present an updated version of the model, Hector V3.2.0 (hereafter Hector V3), and document its new features, implementation of new science, and performance. Significant new features include permafrost thaw, a reworked energy balance submodel, and updated parameterizations throughout. Hector V3 results are in good general agreement with historical observations of atmospheric CO2 concentrations and global mean surface temperature, and the future temperature projections from Hector V3 are consistent with more complex Earth system model output data from the sixth phase of the Coupled Model Intercomparison Project. We show that Hector V3 is a flexible, performant, robust, and fully open-source simulator of global climate changes. We also note its limitations and discuss future areas for improvement and research with respect to the model's scientific, stakeholder, and educational priorities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Neural Networks for Prediction of Complex Chemistry in Water Treatment Process Optimization

Water chemistry plays a critical role in the design and operation of water treatment processes. Detailed chemistry modeling tools use a combination of advanced thermodynamic models and extensive databases to predict phase equilibria and reaction phenomena. The complexity and formulation of these models preclude their direct integration in equation-oriented modeling platforms, making it difficult to use their capabilities for rigorous water treatment process optimization. Neural networks (NN) can provide a pathway for integrating the predictive capability of chemistry software into equation-oriented models and enable optimization of complex water treatment processes across a broad range of conditions and process designs. Herein, we assess how NN architecture and training data impact their accuracy and use in equation-oriented water treatment models. We generate training data using PhreeqC software and determine how data generation and sample size impact the accuracy of trained NNs. The effect of NN architecture on optimization is evaluated by optimizing hypothetical black-box desalination processes using a range of feed compositions from USGS brackish water data set, tracking the number of successful optimizations, and testing the impact of initial guess on the final solution. Our results clearly demonstrate that data generation and architecture impact NN accuracy and viability for use in equation-oriented optimization problems.

Dudchenko, Alexander V↗
DOE OSTI2022

Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O 2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1966

Chart system simplifies identification of complex design assemblies

Identification breakdown chart that lists the component parts required for any specific end item is used to identify rapidly and accurately, from numerous drawings, all the component parts of a complex design assembly. Cylindrical and complex configurations are depicted as continuous flat surfaces for ready identification.

Morin, H. P.↗