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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp

Abstract Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Oxygen reduction reaction catalysts prepared by platinizing thermally activated zeolitic imidazolate frameworks

In this study, highly efficient and low-cost oxygen reduction reaction (ORR) catalyst is essential to improve the cost competitiveness of the proton-exchange membrane fuel cells (PEMFCs). One potential approach of cost reduction is to apply low loading Pt over a catalytically active support made of platinum metal group free (PGM-free) material to compensate the overall ORR activity through synergistic catalysis between Pt and PGM-free support. In this report, we investigated a series of catalysts prepared by adding low-loading Pt over ORR active support prepared through thermally activated Co/Zn methyl-imidazolate framework (Co/Zn-ZIF) at various Co/Zn ratios. Catalytic activity measurement and structural characterization were performed in an attempt to gain better understanding of certain structural factors that could influence the catalytic performance.

25 ENERGY STORAGE↗
DOE OSTI2023

Effect of the Molecular Structure of Surface Vanadia on Activity and Regenerability of VO $x$ /In 2 O 3 Catalysts for CO 2 -Assisted Oxidative Dehydrogenation of Propane

Our recent work has reported that higher propylene selectivity and improved stability can be achieved by combining redox-active VO $x$ and basic In 2 O 3 for CO 2 -assisted oxidative dehydrogenation of propane (CO 2 -ODHP). In the present work, we continued to explore the stability and regenerability of V/In catalysts. In particular, our interest lies in identifying the effect of mono- and polyvanadate on catalytic performance and regenerability. A V/In catalyst with an increased proportion of monovanadate was prepared using the Schlenk line under moisture-free conditions (V/In–S), while the fully polymerized vanadate catalyst was prepared through a regular impregnation (V/In) for comparison. The Schlenk-line-prepared catalyst, namely, V/In–S, not only exhibits a 17–30% enhanced propylene yield at high temperatures (500–540 °C) over V/In but also presents improved stability and regenerability with nearly 88% activity recovered after regeneration in O 2 . Detailed characterizations have been performed to reveal the catalyst structure–performance relationship, including chemisorption (NH 3 /CO 2 -temperature-programmed desorption, NH 3 /CO 2 -TPD), H 2 -temperature-programmed reduction (H 2 -TPR), and spectroscopic studies [Raman spectroscopy, UV–vis diffuse reflectance spectroscopy (UV–vis DRS), near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS), and high-sensitivity low-energy ion scattering (HS-LEIS)]. Characterization results demonstrate that compared with polyvanadates, monovanadates lead to strengthened interaction with In 2 O 3 and a more stabilized V/In surface and subsurface, as well as improved redox properties of VO $x$ . These advantages give rise to the observed enhancement in activity, stability, and regenerability. In conclusion, these findings advance the understanding of the relationship between the activity/stability and the molecular structure of surface oxide species (vanadia) and the interplay between acid–base interactions and redox properties of mixed metal-oxide catalysts for efficient CO 2 -ODHP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗
DOE OSTI2025

In-situ/operando study of Cu-based nanocatalysts for CO 2 electroreduction using electrochemical liquid cell TEM

The structure of a nanocatalyst during electrocatalytic reactions often deviates from its pristine structure due to intrinsic properties, or physical and chemical adsorption at the catalytic surfaces. Taking Cu-based catalysts for CO 2 electroreduction reactions (CO 2 RR) as an example, they often experience segregation, leaching, and alloying during reactions. With the recent breakthrough development of high-resolution polymer electrochemical liquid cells, in-situ electrochemical liquid cell transmission electron microscopy (EC-TEM) alongside other advanced microscopy techniques, has become a powerful platform for revealing electrocatalysts restructuring at the atomic level. Considering the complex reactions involving electrified solid-liquid interfaces and catalyst structural evolution with intermediates, systematic studies with multimodal approaches are crucial. In this article, we demonstrate a research protocol for the study of electrocatalysts structural evolution during reactions using the in-situ EC-TEM platform. Using Cu and CuAg nanowire catalysts for CO 2 RR as model systems, we describe the experimental procedures and findings. We highlight the platform’s crucial role in elucidating atomic-scale pathways of nanocatalyst restructuring and identifying catalytic active sites, as well as avoiding potential artifacts to ensure unbiased conclusions. Using the multimodal characterization toolbox, we provide the opportunity to correlate the structure of a working catalyst with its performance. Finally, we discuss advancements as well as the remaining gap in elucidating the structural-performance relationship of working catalysts. We expect this article will assist in establishing guidelines for future investigations of complex electrochemical reactions, such as CO 2 RR and other catalytic processes, using the in-situ EC-TEM platform.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fast Proton Insertion in Layered H 2 W 2 O 7 via Selective Etching of an Aurivillius Phase

H 2 W 2 O 7 , a metastable material synthesized via selective etching of the Aurivillius-related Bi 2 W 2 O 9 , is shown as an electrode for high power proton-based energy storage. Comprehensive structural characterization is performed to obtain a high-fidelity crystal structure of H 2 W 2 O 7 using an iterative approach that combines X-ray diffraction, neutron pair distribution function, scanning transmission electron microscopy, Raman spectroscopy, and density functional theory modeling. Electrochemical characterization shows a capacity retention of ≈80% at 1000 mV s –1 (1.5-s charge/discharge time) as compared to 1 mV s –1 (≈16-min charge/discharge time) with cyclability for over 100 000 cycles. Energetics from density functional theory calculations indicate that proton storage occurs at the terminal oxygen sites within the hydrated interlayer. Last, optical micrographs collected during in situ Raman spectroscopy show reversible, multicolor electrochromism, with color changes from pale yellow to blue, purple, and last, orange as a function of proton content. These results highlight the use of selective etching of layered perovskites for the synthesis of metastable transition metal oxide materials and the use of H 2 W 2 O 7 as an anode material for proton-based energy storage or electrochromic applications.

25 ENERGY STORAGE↗
DOE OSTI2022

Predicting Rupture Pressure and Leak Rate of Alloy 600 U-bend Tubes with PWSCC and Comparing with Test Results (Technical Letter Report)

This report summarizes structural integrity work performed for the US NRC that predicts the structural integrity of steam generator (SG) tubes with flaws in the U-bend. The work covers model development and validation for U-bend tubes containing lab-induced primary water stress corrosion cracks (PWSCC). Limit load models for plastic collapse predicting ligament rupture pressure and leak rate of cracked U-bend tubes were developed and validated with pressure tests and finite element analyses (FEAs). Failure pressure and leak rate tests were conducted at room temperature on Alloy 600 U-bend tubes containing flaws located at various locations around the U-bend. Existing models for predicting structural integrity of straight tubes with well defined, rectangular, electro-discharge-machined (EDM) flaws were modified and used to predict the ligament rupture and unstable burst pressures as well as leak rates for the PWSCC flaws in the U-bend section.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Influence of Numerical Modeling Approaches on Damped Behavior of Flexible Beams: Preprint

Composites structures are widely used in aerospace and wind energy applications for their excellent stiffness and strength-to-weight properties. In these structures, structural damping is critical to predict vibration amplitudes, performance, and reliability. Structural damping is of particular interest for slender wings, rotorcraft blades, and wind turbine blades that can exhibit complex vibration phenomena and are frequently modeled with geometrically exact beam theory (GEBT). Standard approaches of stiffness proportional or modal damping merely assign user defined values and cannot predict damping behavior. This work compares stiffness proportional damping to two more advanced damping approaches: modal strain energy and Prony series. The modal strain energy approach uses a sectional analysis tool to calculate the beam stiffness and postprocess internal stresses from GEBT simulations. The internal stresses are then used to calculate modal damping factors. The Prony series is implemented within GEBT to directly model viscoelastic behavior of the composites. These approaches are compared by modeling the evolution of the damping factors of a realistic flexible wind turbine blade with varying rotational speed. Discrepancies between the approaches suggest areas for future modeling development, but differences in nonlinear damping values are less than current uncertainties about the magnitude of structural damping.

17 WIND ENERGY↗
DOE OSTI2025

Conjugation effect of amine molecules in non-aqueous Mg redox flow batteries

Nonaqueous magnesium redox flow batteries (Mg RFBs) are attractive for low-cost, high-energy-density and long-cycle-life stationary energy storage applications. However, state-of-the-art cathode redox-active molecules suffer from low solubility and low redox potential. Herein, we screened a range of cathode redox-active molecules and identified amine molecules as optimal to couple with the Mg anode. The properties of amine derivatives and their performances were collected to establish the correlation between molecular structures and electrochemical performances. The redox potential and solubility of these amine molecules were influenced by the π-conjugated and non-conjugated structures of amine derivatives. Density functional theory (DFT) simulations and the inverse aromatic fluctuation index (FLU −1 ) verified that conjugation had an important role in stabilizing the molecule and increasing its redox potential. Notably, tris[4-(diethylamino)phenyl]amine (TDPA) achieved the highest theoretical energy density (∼120 Wh L −1 ) due to its high solubility (∼0.9 M) and voltage (∼2.5 V vs. Mg/Mg 2+ ). We also demonstrated that ether solvents were crucial for stable, high-solubility catholytes, while bulk anions did not affect the redox potential of these p-type molecules. In a Mg-amine RFB configuration, the battery delivered 2.50 V, a specific discharge capacity of 106.5 mAh g −1 , an initial coulombic efficiency of 90.74%, and a capacity retention of 93.88% after 150 cycles.

Qin, Yunan [University of Utah, Salt Lake City, UT↗
DOE OSTI2021

Epitaxial nanotwinned metals and alloys: synthesis-twin structure–property relations

Extensive studies have been performed to understand the structure–property relationship in nanotwinned (NT) metals, where the average twin thickness or twin spacing is less than 100 nm. NT metals may have high strength, ductility, good electrical conductivity and corrosion resistance and have promising applications in microelectronics, structural materials and coatings for gas and oil industry. Most prior studies focus on the computational and experimental investigations of NT metals with low stacking fault energy (SFE) and often in polycrystalline forms. In this highlight, we review recent findings on epitaxial growth of NT metals and alloys with low and high SFEs deposited on single crystal substrates, and focus primarily on advancing our comprehension towards tailoring the microstructures and properties of NT metals via extrinsic factors, including the synthesis technique, parametric control and growth template, and intrinsic factors, such as SFE and thermodynamic, kinetic alloying effects. The review intends to illuminate how to synthesize and design epitaxial NT structures to achieve desirable properties.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structure-Dependent Lithium Metal Reactivity of Lithium Lanthanum Titanium Oxide Solid Electrolytes

Ongoing efforts to design stable, ionically conductive solid-state electrolytes (SSEs) for next-generation solid-state batteries make it clear that both long and short-range structural order strongly influence materials performance. However, clear structure-property relationships are generally lacking, making it difficult to develop design rules for improving the (electro) chemical stability of SSEs. Here, in this work, we synthesize epitaxial, single-crystal lithium lanthanum titanium oxide (LLTO) films and demonstrate that the kinetics of Ti 4+ reduction and lithium intercalation depend sensitively on the crystal orientation, with electrochemical stability increasing as LLTO (001) < (110) similar to (112) < (100). However, thermodynamic stability is ultimately unaffected-all orientations fully reduce after extended contact with Li metal. In contrast, amorphous LLTO films exhibit minimal, self-limiting reactivity that results in an interface that is stable to extended contact with Li metal. The results demonstrate the potential to engineer crystal lattice strain and long-range order to differentially tune the stability of the solid electrolyte toward reactive lithium metal and cathode materials, suggesting strategies for enabling the wider deployment of LLTO and other ionically conductive ceramic films in advanced energy storage technologies

Ketter, Benjamin [Argonne National Laboratory (ANL↗
DOE OSTI2021

Formation of LiF Surface Layer During Direct Fluorination of High-Capacity Co-Free Disordered Rocksalt Cathodes

Disordered rocksalt (DRX) cathodes have attracted interest due to their high capacity and compositional flexibility (e.g., Co-free chemistries). However, the sloping voltage profile and gradual capacity fade during cycling have hindered widespread adoption of these materials. Simulations predict that fluorine substitution in DRX cathodes will improve their capacity, rate performance and cyclability. In this study we use a fluidized bed reactor to fluorinate a model Lirich DRX composition (Li1.15Ni0.375Ti0.375Mo0.1O2, NTMO) to investigate how fluorine content impacts the cathode’s structure and electrochemical performance. Instead of substituting O with F to form oxyfluoride phases, direct fluorination of DRX cathodes leads to formation of LiF surface films which improves the specific energy and capacity retention. This study demonstrates the feasibility of direct fluorination to improve the electrochemical performance of high voltage cathodes by tuning the material’s surface chemistry.

Co-free disordered rock-salt cathode, direct fluor↗
DOE OSTI2023

Biopolymer‐assisted Synthesis of P‐doped TiO 2 Nanoparticles for High‐performance Lithium‐ion Batteries: A Comprehensive Study

Abstract TiO 2 material has gained significant attention for large‐scale energy storage due to its abundant, low‐cost, and environmentally friendly properties, as well as the availability of various nanostructures. Phosphorus doping has been established as an effective technique for improving electronic conductivity and managing the slow ionic diffusion kinetics of TiO 2 . In this study, non‐doped and phosphorus doped TiO 2 materials were synthesized using sodium alginate biopolymer as chelating agent. The prepared materials were evaluated as anode materials for lithium‐ion batteries (LIBs). The electrodes exhibit remarkable electrochemical performance, including a high reversible capacity of 235 mAh g −1 at 0.1 C and excellent first coulombic efficiency of 99 %. An integrated approach, combining operando XRD and ex‐situ XAS, comprehensively investigates the relationship between phosphorus doping, material structure, and electrochemical performance, reinforced by analytical tools and first principles calculations. Furthermore, a full cell was designed using 2 %P‐doped TiO 2 anode and LiFePO 4 cathode. The output voltage was about 1.6 V with high initial specific capacity of 148 mAh g −1 , high rate‐capability of 120 mAh g −1 at 1 C, and high‐capacity retention of 96 % after 1000 cycles at 1 C.

El Halya, Nabil↗
DOE OSTI2023

Convoluted filtering for process cycle modeling

Principles of materials science and engineering, physics, mathematics, and information science are used to extract knowledge and insights from the process-structure–property-performance relationships hidden in materials data. The process-structure modeling can be accelerated without loss of interpretability, with artificial intelligence tools that mimic the salient features of the process and process-structure relations. In this work, a novel convoluted model-filtering technique was exploited to build and successfully train the Convoluted Filter (CoFi) artifacts for Fe-based alloy heat treatment cycles. The artifacts were pre-trained to filter out deep models that change the surrogate microstructure state after the heat treatment at ambient conditions. Direct representation of the thermal cycle features within knowledge Graph facilitated development of meaningful data models for microstructure evolution, which reduce overfitting to limited datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Automated Adsorption Workflow for Semiconductor Surfaces and the Application to Zinc Telluride

Surface adsorption is a crucial step in numerous processes, including heterogeneous catalysis, where the adsorption of key species is often used as a descriptor of efficiency. We present here an automated adsorption workflow for semiconductors which employs density functional theory calculations to generate adsorption data in a high-throughput manner. Starting from a bulk structure, the workflow performs an exhaustive surface search, followed by an adsorption structure construction step, which generates a minimal energy landscape to determine the optimal adsorbate-surface distance. An extensive set of energy-based, charge-based, geometric, and electronic descriptors tailored toward catalysis research are computed and saved to a personal user database. Finally, the application of the workflow to zinc telluride, a promising CO 2 reduction photocatalyst, is presented as a case study to illustrate the capabilities of this method and its potential as a material discovery tool.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Crosslinked Matrimid®-like polyimide membranes with unimodal network structure for enhanced stability and gas separation performance

Gas separation membranes have attracted academic and industrial attention, and crosslinking has been identified to be one of the most effective ways to enhance membrane stability. In this paper, a series of crosslinked Matrimid®-like films with unimodal network structures are prepared via thermally end-linking phenylethnyl-terminated BTDA-DAPI oligomers with well-controlled molecular weight (i.e., 3000–15,000 g/mol), wherein the crosslink density (the inter-crosslink chain length) of resulting unimodal networks is systematically varied by using oligomers with various molecular weight. Comprehensive characterizations of chemical structure, thermal properties, microstructures are performed. Pure-gas permeation measurements are performed focusing on H 2 /CH 4 and CO 2 /CH 4 separations as a function of crosslink density. In sharp contrast to the commonly observed permeability reduction in randomly crosslinked networks, all the crosslinked unimodal films, even when densely crosslinked, present markedly enhanced permeability and well-maintained ideal selectivity relative to the uncrosslinked linear counterpart, leading to almost horizontal movements towards upper bounds along with expectedly enhanced membrane stability. In conclusion, it is concluded that introducing bulky groups at the crosslink sites provide a practical means to counteract the densification effect induced by crosslinking and the construction of unimodal networks exemplifies a fundamentally new strategy to regulate the microstructure and property of crosslinked membranes for gas separations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

On the performance of composite schemes in determining equilibrium molecular structures

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, in this study, the performance of two different ab initio composite approaches for obtaining equilibrium structures, “energy scheme” and “geometry scheme,” is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

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

3D-equivariant graph neural networks for protein model quality assessment

Quality assessment (QA) of predicted protein tertiary structure models plays an important role in ranking and using them. With the recent development of deep learning end-to-end protein structure prediction techniques for generating highly confident tertiary structures for most proteins, it is important to explore corresponding QA strategies to evaluate and select the structural models predicted by them since these models have better quality and different properties than the models predicted by traditional tertiary structure prediction methods. We develop EnQA, a novel graph-based 3D-equivariant neural network method that is equivariant to rotation and translation of 3D objects to estimate the accuracy of protein structural models by leveraging the structural features acquired from the state-of-the-art tertiary structure prediction method—AlphaFold2. We train and test the method on both traditional model datasets (e.g. the datasets of the Critical Assessment of Techniques for Protein Structure Prediction) and a new dataset of high-quality structural models predicted only by AlphaFold2 for the proteins whose experimental structures were released recently. Our approach achieves state-of-the-art performance on protein structural models predicted by both traditional protein structure prediction methods and the latest end-to-end deep learning method—AlphaFold2. It performs even better than the model QA scores provided by AlphaFold2 itself. The results illustrate that the 3D-equivariant graph neural network is a promising approach to the evaluation of protein structural models. Integrating AlphaFold2 features with other complementary sequence and structural features is important for improving protein model QA.

59 BASIC BIOLOGICAL SCIENCES↗