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At least 397 records · Page 22

Metabolite Damage and Damage Control in a Minimal Genome

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean

Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent oil production and a diverse microbial community associated with the degradation of petroleum. Here, we combine DNA-based stable-isotope probing (DNA-SIP) with metagenomics to elucidate the metabolic underpinnings of native alkane-degrading bacteria from the FSC. From two 13C n-hexadecane SIP experiments using seawater from 5 and 700 m depths in the FSC, we obtained 42 metagenome-assembled genomes (MAGs) belonging to 19 genera, including two previously overlooked hydrocarbon-degrading bacteria, Lentibacter (Alphaproteobacteria) and Dokdonia (Bacteroidetes). Diversity surveys indicated Lentibacter were dominant members of the FSC, constituting up to 17% of these communities. Many of the SIP-enriched MAGs (20/42) encoded a complete alkane oxidation pathway, including alkane monooxygenase (AlkB), rubredoxin reductase (AlkT), and rubredoxin-2 (AlkG). Fourteen Aphaproteobacteria MAGs lacked AlkG for electron transfer. Instead, they encoded novel disulfide isomerases with iron-binding cysteine motifs conserved across rubredoxins. Dokdonia lacked AlkT and AlkG, however, their central alkane-degradation catabolic pathways were complete. We describe previously unrecognized bacteria capable of hydrocarbon degradation, including the dominant genera Lentibacter, which may continuously purge hydrocarbons released from oil exploration activities in the FSC. This advances the understanding of the diversity and physiologies of alkane degradation in the North Atlantic and provides evidence of new mechanisms used to metabolize alkanes.

59 BASIC BIOLOGICAL SCIENCES↗

PNNL-Predictive-Phenomics/ProCaliper

ProCaliper is a Python library that curates, organizes, and computes protein structure features in a way that easily interfaces with user-provided experimental data. It extracts or computes protein binding site, active site, charge, pLDDT (order/disorder), acid dissociation, protonation, solvent accessible surface area, disulfide bond distance, and protein secondary structure data using precomputed protein structures and publicly available databases. It provides a unified API for integrating additional residue-level data and for visualizing residue features in 3D.

Rozum, Jordan [Pacific Northwest National Lab]↗

Classification of Semiconductors Using Photoluminescence Spectroscopy and Machine Learning

Photoluminescence spectroscopy is a nondestructive optical method that is widely used to characterize semiconductors. In the photoluminescence process, a substance absorbs photons and emits light with longer wavelengths via electronic transitions. This paper discusses a method for identifying substances from their photoluminescence spectra using machine learning, a technique that is efficient in making classifications. Neural networks were constructed by taking simulated photoluminescence spectra as the input and the identity of the substance as the output. Here, six different semiconductors were chosen as categories: gallium oxide (Ga 2 O 3 ), zinc oxide (ZnO), gallium nitride (GaN), cadmium sulfide (CdS), tungsten disulfide (WS 2 ), and cesium lead bromide (CsPbBr 3 ). The developed algorithm has a high accuracy (>90%) for assigning a substance to one of these six categories from its photoluminescence spectrum and correctly identified a mixed Ga 2 O 3 /ZnO sample.

47 OTHER INSTRUMENTATION↗

Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens

HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.

60 APPLIED LIFE SCIENCES↗

The electronic states of ITO–MoS2: Experiment and theory

Abstract We report a combination of experimental results with density functional theory (DFT) calculations to understand electronic structure of indium tin oxide and molybdenum disulfide (ITO–MoS 2 ) interface. Our results indicate ITO and MoS 2 conform an n-type Schottky barrier of c.a. − 1.0 eV due to orbital interactions; formation of an ohmic contact is caused by semiconducting and metal behavior of ITO as a function of crystal plane orientation. ITO introduces energy levels around the Fermi level in all interface models in the Γ-Μ-Κ-Γ path. The resulted Van der Waals interface and the values of Schottky barrier height enhance electron carrier injection. Graphical abstract

López-Galán, Oscar A. (ORCID:0000000292912562)↗

Materials Data on H3CS by Materials Project

CH3S crystallizes in the monoclinic P2_1/c space group. The structure is zero-dimensional and consists of four dimethyl disulfide molecules. there are two inequivalent C3+ sites. In the first C3+ site, C3+ is bonded in a trigonal non-coplanar geometry to three H+0.33- and one S2- atom. All C–H bond lengths are 1.10 Å. The C–S bond length is 1.82 Å. In the second C3+ site, C3+ is bonded in a trigonal non-coplanar geometry to three H+0.33- and one S2- atom. All C–H bond lengths are 1.10 Å. The C–S bond length is 1.82 Å. There are six inequivalent H+0.33- sites. In the first H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the second H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the third H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the fourth H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the fifth H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the sixth H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. There are two inequivalent S2- sites. In the first S2- site, S2- is bonded in a water-like geometry to one C3+ and one S2- atom. The S–S bond length is 2.04 Å. In the second S2- site, S2- is bonded in a water-like geometry to one C3+ and one S2- atom.

36 MATERIALS SCIENCE↗

Materials Data on H3CS by Materials Project

CH3S crystallizes in the monoclinic P2_1/c space group. The structure is zero-dimensional and consists of four dimethyl disulfide molecules. there are two inequivalent C3+ sites. In the first C3+ site, C3+ is bonded in a trigonal non-coplanar geometry to three H+0.33- and one S2- atom. All C–H bond lengths are 1.10 Å. The C–S bond length is 1.82 Å. In the second C3+ site, C3+ is bonded in a trigonal non-coplanar geometry to three H+0.33- and one S2- atom. All C–H bond lengths are 1.10 Å. The C–S bond length is 1.82 Å. There are six inequivalent H+0.33- sites. In the first H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the second H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the third H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the fourth H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the fifth H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. In the sixth H+0.33- site, H+0.33- is bonded in a single-bond geometry to one C3+ atom. There are two inequivalent S2- sites. In the first S2- site, S2- is bonded in a water-like geometry to one C3+ and one S2- atom. The S–S bond length is 2.04 Å. In the second S2- site, S2- is bonded in a water-like geometry to one C3+ and one S2- atom.

36 MATERIALS SCIENCE↗

Materials Data on S by Materials Project

S is Modderite-derived structured and crystallizes in the trigonal P3 space group. The structure is zero-dimensional and consists of four 1,2,3-trithiacyclopropane molecules and three hydrogen disulfide molecules.

36 MATERIALS SCIENCE↗

Materials Data on CS30 by Materials Project

S30C crystallizes in the monoclinic C2/m space group. The structure is zero-dimensional and consists of twelve hydrogen disulfide molecules, eight hydrogen sulfide molecules, two CS2 clusters, and eight S clusters. In each CS2 cluster, C4+ is bonded in a linear geometry to two equivalent S+0.13- atoms. Both C–S bond lengths are 1.55 Å. S+0.13- is bonded in a single-bond geometry to one C4+ atom. In each S cluster, there are three inequivalent S+0.13- sites. In the first S+0.13- site, S+0.13- is bonded in a single-bond geometry to two S+0.13- atoms. There are one shorter (1.90 Å) and one longer (3.69 Å) S–S bond lengths. In the second S+0.13- site, S+0.13- is bonded in a single-bond geometry to two S+0.13- atoms. The S–S bond length is 3.85 Å. In the third S+0.13- site, S+0.13- is bonded in a 1-coordinate geometry to two S+0.13- atoms.

36 MATERIALS SCIENCE↗

Materials Data on S by Materials Project

S is gamma nitrogen-like structured and crystallizes in the tetragonal P4_2/m space group. The structure is zero-dimensional and consists of two hydrogen disulfide molecules. S is bonded in a single-bond geometry to one S atom. The S–S bond length is 1.89 Å.

36 MATERIALS SCIENCE↗

Materials Data on CaSnS3 by Materials Project

CaSn(S)3 crystallizes in the monoclinic C2 space group. The structure is zero-dimensional and consists of four 7440-31-5 molecules, four calcium molecules, four hydrogen disulfide molecules, and four hydrogen sulfide molecules.

36 MATERIALS SCIENCE↗

Polymer Composites Reinforced by Carbon-Allotrope Fillers for Selective Laser Sintering (SLS) - A Review

The limited commercial availability of applicable polymer powders has hindered the widespread implementation of SLS as a legitimate manufacturing method. This is partly due to the mechanism of SLS, which requires powders to meet rigid specifications if processing is to be successful. Furthermore, powders that do meet requirements are often incapable of producing quality, high-performance parts. Academic and industrial research has focused on composite development to overcome this problem. The incorporation of fillers including calcium carbonate, molybdenum disulfide, and aluminum have all been found to influence the processing behavior of PA12 powder and ultimately, the properties of the final part.3-5 Here, the thermal and mechanical properties of sintered composite parts produced using polymer powders reinforced by various carbon-based fillers is discussed.

36 MATERIALS SCIENCE↗

Understanding Topological Pseudospin Transport in Van Der Waals' Materials

Because of symmetry, crystals often have degenerate valleys in the conduction or the valence band. This “valley” degree of freedom, similar to electronic charge and spin, has been proposed as an information carrier for new classes of electronic and optoelectronic devices. The basic requirement of information processing is to be able to create and manipulate a flow of valley pseudospin, i.e. valley pseudospin current. Valley pseudospin currents have been demonstrated in recent experiments in monolayer molybdenum disulfide and graphene on hexagonal boron nitride. However, the key fundamental questions regarding the nature of valley pseudospin transport remain open. This project will investigate the importance of Berry curvature effects in valley pseudospin transport and explore regimes for quantized valley Hall conductivity and pure valley pseudospin currents. The study will rely on combined optical and electrical transport techniques to create, manipulate and detect valley pseudospin currents in two-dimensional (2D) van der Waals’ materials of hexagonal structure. The insights provided by this research will deepen the understanding of valley pseudospin transport in 2D and help the development of novel valley-based technologies.

36 MATERIALS SCIENCE↗

Controlling Structural, Electronic, and Energy Flow Dynamics of Catalytic Processes through Tailored Nanostructures

MoS 2 (molybdenum disulfide) is a highly-versatile catalyst material for support of numerous reactions from hydrodesulfurization and denitrogenation to the focus of this renewal proposal: hydrogenation of CO/CO 2 towards (higher) alcohols. At the same time, MoS 2 is a non-toxic, environmentally-benign and rather inert material- which under ambient conditions for some time has served as a lubricant and, more recently, as next-generation electronic material. The apparent contrast between inertness and stability in ambient, and catalytic activity under reactive conditions is puzzling and calls for a synergistic theoretical and experimental investigation with the long-term objective of enabling the rational design of MoS 2 -based catalysts for alcohol-formation reactions by providing a microscopic understanding of the environmental factors that determines site activity and selectivity. Our research project seeks answers to the questions (a) what conformation does MoS 2 adopt under reaction conditions (as opposed to that under ultrahigh vacuum and low temperatures)?; (b) what reaction pathways exist on such a material?; (c) how can the local environment of the active sites be manipulated so as to make MoS 2 an efficient catalyst for production of higher alcohol from syngas? In particular, research strategies will explore how the basal plane composed of sulfur atoms can be activated so as to exhibit a reactivity of its own, by addressing three research targets and building on extensive preliminary and enabling work: (1) vacancies and vacancy aggregates on the basal plane; (2) non-local catalyst transformation through alkali doping, hydrogenation and phase transition; (3) fabrication of a metal-nanoparticle-activated MoS 2 system, in which particle anchoring, reactive sites and pathways as well as selectivity are controlled by design, as an example of predictive development of a catalyst material,. All strategies are directed to improve the efficacy of the key reactive sites and selectivity of chemical pathways by design, to replace the inefficient methodology of trial and error in catalyst development. This research project represents a synergistic combination of computational guidance, foundational surface-science-based experiments and validation under reactive conditions that aims at transformative new insights into the working of MoS 2 -based hydrogenation-catalysts, a topic squarely at the center of the interest of DOE BES. Guided and led by Talat Rahman, a computational physicist, this project will apply density functional theory to understand structure, reaction pathways and chemical potentials associated with MoS 2 -based CO/CO 2 hydrogenation, augmented by kinetic Monte Carlo methods for reaction rates and prefactors as well as ab-initio molecular dynamics for evaluation of thermal stability. Complementary experimental input and validation will originate from co-PI Ludwig Bartels, a physical chemist and materials scientist, whose group focuses on local imaging and preparation of MoS 2 materials, from co-PI Peter Dowben, an experimental physicist, whose group is expert in the spectroscopy of occupied and unoccupied electronic states, and from senior collaborator Michael White of Brookhaven National Laboratory, whose group generates high-resolution electronic and activity information on size-selected well-defined metal chalcogenide clusters. This collaborative effort will enable a comprehensive understanding of the correlation of structural integrity and catalytic activity of MoS 2 in forms ranging from extended films to individual particles with known geometries and binding sites. Alcohol formation from syngas is a rapidly emerging application that has great potential through facile, economic, and decentralized biomass gasification. CO 2 activation is one of the most pressing concerns of our time: increasing CO 2 levels in the atmosphere change the climate and expose the globe to environmental transformations with the potential for enormous economic and societal impact. We will investigate CO/CO 2 hydrogenation via an interdisciplinary research collaboration with established synergy – one that, in accordance with the mission of the DOE, involves accredited Hispanic-Serving Institutions and that, through student exchange with international collaborators and National Labs, will directly benefit a broad spectrum of communities and generate human resources in sciences essential to their future.

2D materials↗

Impact of Radiation on the Electronic Structure of MoS 2

Electrons in a semiconductor occupy states within certain energy ranges, called energy bands. The position of the Fermi level with respect to these energy bands determines the charge carrier type of the semiconductor. Molybdenum disulfide (MoS 2 ) is a two-dimensional, n-type semiconductor with potential applications in flexible electronics, transparent electronics, and optoelectronics. Electronic devices containing MoS 2 could be used in environments where radiation affects device performance. Thus, it is important to determine the impact of radiation on MoS 2 . A one-molecule-thick layer of MoS 2 (monolayer) and a two-molecule-thick layer of MoS 2 (bilayer) were placed onto different areas of a gold (Au) substrate containing 1.2-µm-deep holes. The MoS 2 was suspended over these holes but supported by the Au elsewhere on the substrate. This sample configuration was used to determine the effect of He + radiation on the electronic properties of the suspended MoS 2 and the Au-supported MoS 2 . The MoS 2 was irradiated by He+ ions in two stages. The energy bands of the MoS 2 were measured with respect to the Fermi level via photoelectron emission microscopy before irradiation and after each irradiation stage. From each measurement, the charge carrier type of the MoS 2 after the corresponding irradiation stage was determined. The Fermi levels of the suspended monolayer and bilayer decreased by ≈0.15 eV with respect to the bands during the first irradiation stage During the second irradiation stage, however, the Fermi levels didn’t change significantly. This lack of change supports the existence of a radiation threshold, above which the electronic properties of suspended MoS 2 remain the same. The Fermi levels of the supported monolayer and bilayer increased over the cumulative irradiation and didn’t show evidence of a threshold. Thus, suspended MoS 2 becomes less n-type as it is irradiated. Supported MoS 2 , however, becomes more n-type as it is irradiated. These results could inform the development of radiation tolerance standards for MoS 2 , and thus, radiation-tolerant MoS 2 -based electronics.

36 MATERIALS SCIENCE↗

Tritium Producing Burnable Absorber Rod (TPBAR) Cutterhead Test Report

The Tritium Extraction Facility (TEF) Target Rod Preparation (TRP) Tritium Producing Burnable Absorber Rod (TPBAR) Cutterhead is a specialized remote tubing cutter used to breach TPBARs (approximately 0.381 inch outside diameter x 0.336 inch inside diameter 316 stainless steel tubing). The cutterhead was originally designed by an external engineering firm - RTS Wright Industries. The bearing housing and drive plate, the main drive components, are designed to be fabricated from Nitronic 60, an anti-galling stainless steel, and coated with Dicronite® (Tungsten Disulfide) lubricating coating. These parts have galled after a limited number of cycles, damaging the fine 3.25-32 UN threads which drive the system. In some cases, destructive sectioning is required to remove the failed parts from the cutterhead. Cutterheads have been fabricated by multiple machine shops, with some cutterheads failing very quickly and some lasting more than 1,000 cuts. In 2019, Emery Corporation, now Toner Machining Technologies (TMT) was contracted to fabricate four (4) new complete sets of cutterheads. The newly fabricated cutterheads have not been able to pass the required acceptance test without the bearing housing and drive plate threads galling. TMT has tried multiple sets of Nitronic 60 bearing housing and drive plates; all have galled after less than 10 cuts.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗