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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Relaxation and Aging of Nanosphere Assemblies at a Water–Oil Interface

The relaxation and aging of an assembly of spherical nanoparticles (NPs) at a water-oil interface are characterized in situ by grazing incidence X-ray photon correlation spectroscopy. The dynamics of the interfacial assembly is measured while the interface saturates with NPs. Weak attractions between NPs lead to gel-like structures in the assembly, where the in-plane ordering is inhibited by the broad size distribution of the NPs. Structural rearrangements on the length scale of the NP-NP center-to-center distances proceed by intermittent fluctuations instead of continuous cooperative motions. Here, the coexistence of rapid and slow NP populations is confirmed, as commonly observed in soft glass-forming materials. Dynamics are increasingly slowed as the NPs initially segregate to the locally clustered interface. The structural relaxation of the NPs in these localized clusters is 5 orders of magnitude slower than that of free particles in the bulk. When the interface is nearly saturated, the time for relaxation increases suddenly due to the onset of local jamming, and the dynamics slow exponentially afterward until the system reaches collective jamming by cooperative rearrangements. This investigation provides insights into structural relaxations near the glass transition and the evolution of the structure and dynamics of the assemblies as they transition from an isotropic liquid to a dense disordered film.

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

Too big, too small, or just right? A benchmark assessment of density functional theory for predicting the spatial extent of the electron density of small chemical systems

Multipole moments are the first-order responses of the energy to spatial derivatives of the electric field strength. The quality of density functional theory prediction of molecular multipole moments thus characterizes errors in modeling the electron density itself, as well as the performance in describing molecules interacting with external electric fields. However, only the lowest non-zero moment is translationally invariant, making the higher-order moments origin-dependent. Therefore, instead of using the 3 × 3 quadrupole moment matrix, we utilize the translationally invariant 3 × 3 matrix of second cumulants (or spatial variances) of the electron density as the quantity of interest (denoted by K). The principal components of K are the square of the spatial extent of the electron density along each axis. A benchmark dataset of the principal components of K for 100 small molecules at the coupled cluster singles and doubles with perturbative triples at the complete basis set limit is developed, resulting in 213 independent K components. The performance of 47 popular and recent density functionals is assessed against this Var213 dataset. Several functionals, especially double hybrids, and also SCAN and SCAN0 predict reliable second cumulants, although some modern, empirically parameterized functionals yield more disappointing performance. The H, Li, and Be atoms, in particular, are challenging for nearly all methods, indicating that future functional development could benefit from the inclusion of their density information in training or testing protocols.

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

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fischer-Tropsch Synthesis: The Characterization and Testing of Pt-Co/SiO 2 Catalysts Prepared with Alternative Cobalt Precursors

Different low-cost cobalt precursors (acetate, chloride) and thermal treatments (air calcination/H 2 reduction versus direct H 2 -activation) were investigated to alter the interaction between cobalt and silica. H 2 -activated catalysts prepared from cobalt chloride had large Co 0 particles (XRD, chemisorption) formed by weak interactions between cobalt chloride and silica (temperature programmed reduction (TPR), TPR with mass spectrometry (TPR-MS), TPR with extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge spectroscopy (XANES) techniques) and retained Cl-blocked active sites, resulting in poor activity. In contrast, unpromoted Co/SiO 2 catalysts derived from cobalt acetate had strong interactions between Co species and silica (TPR/TPR-MS, TPR-EXAFS/XANES); adding Pt increased the extent of the Co reduction. For these Pt-promoted catalysts, the reduction of uncalcined catalysts was faster, resulting in larger Co 0 clusters (19.5 nm) in comparison with the air-calcined/H 2 -activated catalyst (7.8 nm). Both catalysts had CO conversions 25% higher than that of the Pt-promoted catalyst prepared in the traditional manner (air calcination/H 2 reduction using cobalt nitrate) and three times higher than that of the traditional unpromoted Co/silica catalyst. The retention of residual cobalt carbide (observed in XANES) from cobalt acetate decomposition impacted performance, resulting in a higher C 1 –C 4 selectivity (32.2% for air-calcined and 38.7% for uncalcined) than that of traditional catalysts (17.5–18.6%). The residual carbide also lowered the α-value and olefin/paraffin ratio. Future work will focus on improving selectivity through oxidation–reduction cycles.

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

Topological data analysis of task-based fMRI data from experiments on schizophrenia

We use methods from computational algebraic topology to study functional brain networks, in which nodes represent brain regions and weighted edges represent similarity of fMRI time series from each region. With these tools, which allow one to characterize topological invariants such as loops in high-dimensional data, we are able to gain understanding into low-dimensional structures in networks in a way that complements traditional approaches based on pairwise interactions. In the present paper, we analyze networks constructed from task-based fMRI data from schizophrenia patients, healthy controls, and healthy siblings of schizophrenia patients using persistent homology, which allows us to explore the persistence of topological structures such as loops at different scales in the networks. We use persistence landscapes, persistence images, and Betti curves to create output summaries from our persistent-homology calculations, and we study the persistence landscapes and images using k-means clustering and community detection. Based on our analysis of persistence landscapes, we find that the members of the sibling cohort have topological features (specifically, their 1-dimensional loops) that are distinct from the other two cohorts. From the persistence images, we are able to distinguish all three subject groups and to determine the brain regions in the loops (with four or more edges) that allow us to make these distinctions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Characterizing manufacturing sector disruptions with targeted mitigation strategies

It has become clear in recent decades that manufacturing supply chains are increasingly vulnerable to disruptions of varying geographical scales and intensities. These disruptions—whether intentional, accidental, or resulting from natural disasters—cause failures and capacity reductions to manufacturing infrastructure, with lasting effects that can cascade throughout the manufacturing network. An overall lack of understanding of solutions to mitigate disturbances has rendered the challenge of reducing manufacturing supply chain vulnerability even more difficult. Additionally, the variability of disruptions and their impacts complicates policy maker and stakeholder efforts to plan for specific disruptive scenarios. It is necessary to comprehend different kinds of disturbances and group them based on stakeholder-provided metrics to support planning processes and modeling efforts that promote adaptable, resilient manufacturing supply chains. This paper reviews existing methods for risk management in manufacturing supply chains and the economic and environmental impacts of disruptions. In addition, we develop a framework using agglomerative hierarchical clustering to classify disruptions using U.S. manufacturing network data between 2000 and 2021 and characteristic metrics defined in the literature. Our review identifies five groups of disruptions and discusses both general mitigation methods and strategies targeting each identified group. Further, we highlight gaps in the literature related to estimating and including environmental costs in disaster preparedness and mitigation planning. We also discuss the lack of easily available metrics to quantify environmental impacts of disruptions and how such metrics could be included into our methodology.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

A comparative study between real-world and laboratory accelerated aging of Cu/SSZ-13 SCR catalysts

Elucidating aging mechanisms in real-world applications is a critical component for developing and maintaining Cu/SSZ-13 SCR catalysts. To reveal gaps between laboratory accelerated aging and real-world aging, herein we report thorough comparative studies between 6 representative catalysts. Here, we apply a wide range of catalyst characterization methods, including surface area/porosity analysis, X-ray diffraction (XRD), H 2 -temperature programmed reduction, NH3-temperaure programmed desorption, solid-state nuclear magnetic resonance (NMR), in situ X-ray photoelectron (XPS) and electron paramagnetic resonance (EPR) spectroscopies, to gain atomic-level knowledge on Cu transformation under different aging protocols. We then correlate such knowledge to SCR, NH 3 /NO oxidation kinetic behavior of the catalysts. We found that sulfur aging plays the most important role in interpreting catalyst degradation during real-world application, including direct sulfur poisoning of isolated Cu II SCR active species to CuSO 4 -like species, the agglomeration of such species to multinuclear CuSO 4 clusters, and eventually, CuO formation during desulfation treatments. Such chemistries convert SCR active Cu to SCR inert Cu moieties without severely deteriorating catalyst support integrity. These characteristics are partially replicated by hydrothermal aging in the presence of SOx but are poorly mimicked by hydrothermal aging alone.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Pressure Effects on the Relaxation of an Excited Ethane Molecule in High-Pressure Bath Gases

Here, we use molecular dynamics to calculate the rotational and vibrational energy relaxation of C 2 H 6 in Ar, Kr, and Xe bath gases over a pressure range of 10 to 400 atm and at temperatures of 300 K and 800 K. The C 2 H 6 is instantaneously excited by 80 kcal/mol randomly distributed into both vibrational and rotational modes. The computed relaxation rates show little sensitivity to the identity of the noble gas in the bath. Vibrational relaxation rates show a non-linear pressure dependence at 300 K. At 800 K the reduced range of bath gas densities covered by the range of pressures do not yet show any non-linearity in the pressure dependence. Rotational relaxation is characterized with two relaxation rates. The slower rate is comparable to the vibrational relaxation rate. The faster rate has a linear pressure dependence at 300 K but an irregular, nonlinear pressure dependence at 800 K. To understand this, a model was developed based on approximating the periodic box used in the molecular dynamics simulations by an equal-volume collection of cubes where each cube is sized to allow only single occupancy by the noble gas or the molecule. Combinatorial statistics then leads to a pressure and temperature dependent analytic distribution of the bath gas species the molecule encounters in a collision. This distribution, the dissociation energy of molecule/bath gas complexes and bath gas clusters, and the computed energy release per collision combine to show that only at 300 K is the energy release sufficient to dissociate likely complexes and clusters. This suggests that persistent and pressure-dependent clusters and complexes at 800 K may be responsible for the non-linear pressure dependence of rotational relaxation.

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

Ultrafast visualization of phase transitions in nonequilibrium warm dense matter

Intense ultrafast laser excitation brings materials into highly nonequilibrium states with complex solid–liquid phase transitions. These ultrafast processes yield warm dense matter (WDM) conditions characterized by comparable thermal and Fermi energies, and strong ion–ion coupling. Here, we review recent studies employing mega-electron-volt ultrafast electron diffraction to resolve the structural dynamics of nonequilibrium WDM created by femtosecond laser heating of solids. Furthermore, for the study of warm dense gold, the results showed homogeneous melting that occurs within tens of picoseconds at absorbed energy densities of 0.4–1.4 MJ/kg. These results constrained the electron–ion coupling rate and revealed the melting sensitivity to nucleation seeds. For the study of radiation-damaged tungsten, the results showed a melting transition below the melting temperature. Molecular dynamics simulations suggested that this melting behavior is driven by vacancy defect clusters from radiation damage. These studies provided atomic-level insights into the melting behavior of materials under extreme conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Radical SAM enzymes: Nature's choice for radical reactions

Enzymes that use a [4Fe-4S] 1+ cluster plus S-adenosyl-L-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5´-deoxyadenosyl (5´-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5´-adenosyl bond. Ω liberates 5´-dAdo• through homolysis of the Fe-C5´ bond, in analogy to Co-C5´ bond homolysis in B12, previously viewed as biology’s paradigmatic radical generator. The 5´-dAdo• has been trapped and characterized in radical SAM enzymes via a recently-discovered photoreactivity of the [4Fe- 4S] + /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5´-dAdo• originates in the JahnTeller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5´-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.

deoxyadenosyl radical↗
DOE OSTI2023

Disorder, interactions, and their interplay in novel narrow-gap Dirac materials and Weyl semimetals

Progress of the modern day condensed matter physics is to a large extent driven by the synthesis of new materials, advances in their experimental characterization and theoretical description. Recent discoveries of novel gapless Weyl semimetals, such as NaBi,CdAs, and BiTe-based films, in which magnetic dopants essentially suppress the gap, have added to the family of graphene and topological insulators actively investigated over the past decade. With the field of novel semimetals rapidly maturing, its focus necessarily shifts from demonstrations of the feasibility of such materials to their quantitative characterization. While the transport and optical properties of graphene and topological insulators are well captured within the picture of free non-interacting electrons, gapless 3D Weyl semimetals and narrow-gap 2D semiconductors with Dirac spectrum are known to be extremely susceptible to disorder and electron-electron interactions. This susceptibility obscures the manifestations of nontrivial band structure -- like quantum anomalous Hall effect -- of the new topological materials. Among particular projects to be addressed are: 1) optical conductivity of 3D gapless Dirac fermions in the presence of smooth disorder, 2) interplay of disorder and Coulomb interactions in the spectral properties of such fermions, 3) formation and structure of the impurity band with Coulomb supercritical clusters, 4) Coulomb interaction-driven renormalization of the electron spectrum and of the transport response in the presence of strong magnetic field, 5) instanton approach to the disorder-induced fluctuation states in zero-gap 3D materials, and 6) the role of disorder in quantum anomalous Hall effect. The proposal relies upon the investigators' previous broad expertise in interacting and disordered electron systems. The methods to be employed include perturbative diagrammatic technique, non-perturbative instanton and self-consistent approximations, hydrodynamics of electron liquid. Both analytical as well as numerical approaches are to be employed. The anticipated broader outcome of the proposal includes gaining an in-depth understanding of the interplay of the disorder and interactions under the conditions when this interplay has the most dramatic impact on observables. Traditionally, interaction effects are among the most challenging and interesting problems of condensed matter physics. Similarly, disordered systems typically present very difficult but extremely rich problems in the description of various materials. Importantly, understanding the spectral and transport properties of such materials not only presents the fundamental objective, but is also of particular interest for many applications, such as computation, memory, optics, plasmonics. In particular realization of the quantum anomalous Hall effect may lead to the development of low-power-consumption electronics. Indeed, a major constraint for practical use of the quantum Hall effect is limited by the requirement of the quantizing magnetic field. At the same time, the quantum anomalous Hall effect samples exhibit non-dissipative edge quantum transport in a zero magnetic field.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Detailed Characterization of Vitrinite-Rich Subbituminous and Bituminous Coals for Utilization in Carbon Fiber Precursor Production

Chemical structures of candidate coals (one subbituminous coal from the Powder River Basin and three bituminous Eastern US coals) were examined for potential low-cost carbon fiber precursor production. Here, the structural evaluation examined the carbon skeleton ( 13 C nuclear magnetic resonance (NMR) and high-resolution transmission electron microscopy (HRTEM)), the heteroatom functionality (X-ray photoelectron spectroscopy (XPS) Fourier transform infrared spectroscopy (FTIR) and NMR), the structural ordering and distribution of PAH sizes (HRTEM), and an estimation of the molecular weight distribution (laser desorption ionization mass spectrometry, LDIMS). The molecular compositional distributions were also evaluated for a mixed solvent extract (atmospheric pressure photoionization, 21 T Fourier transform ion cyclotron resonance mass spectrometry, FT-ICR MS). Significant structural differences existed between the subbituminous and bituminous coals, as expected with coalification (with the bituminous coals having a higher carbon content, lower oxygen content, higher aromaticity values, larger cluster sizes, and so forth). While the bituminous coals were similar in structure (close in rank with Blue Gem being hvAb and the rest being hvBb), structural differences were still evident. Specifically, structural similarities were evident for the average properties of Herrin and Springfield coals: same rank, similar moisture, and volatile matter yields, along with similar aromaticity and carbon and hydrogen content. However, significant structural differences were observed at the molecular level by 21 T FT-ICR MS, which showed that the Springfield coal was structurally more complex. Specifically, 21740, 16931, 30190, and 12982 unique elemental compositions were identified for the Monarch, Herrin, Springfield, and Blue Gem coals, further illustrating the complexity of the coal.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States

The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Atom Probe Tomography Investigation of Clustering in Model P 2 O 5 -Doped Borosilicate Glasses for Nuclear Waste Vitrification

Atom probe tomography (APT) has been utilized to investigate the microstructure of two model borosilicate glasses designed to understand the solubility limits of phosphorous pentoxide (P 2 O 5 ). This component is found in certain high-level radioactive defence wastes destined for vitrification, where phase separation can potentially lead to a number of issues relating to the processing of the glass and its long-term chemical and structural stability. The development of suitable focused ion beam (FIB)-preparation routes and APT analysis conditions were initially determined for the model glasses, before examining their detailed microstructures. In a 3.0 mol% P 2 O 5 -doped glass, both visual inspection and sensitive statistical analysis of the APT data show homogeneous microstructures, while raising the content to 4.0 mol% initiates the formation of phosphorus-enriched nanoscale precipitates. This study confirms the expected inhomogeneities and phase separation of these glasses and offers routes to characterizing these at near-atomic scale resolution using APT.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Novel Wavefunction Approaches for Studying Actinides and Other Heavy Elements (Final Report (2012-2020))

The theoretical characterization of actinide molecules is a crucial complement to their experimental study; actinides are vital to issues of national security and energy, but they are expensive and hazardous to study experimentally. However, because actinides contain a large number of electrons and are often strongly correlated, their theoretical description is difficult. We have had success studying actinide chemistry and physics using density functional theoretical approaches over the past several years, but we have found that such methods are incapable of treating strong correlations adequately. We thus shifted our research focus to the development of tractable wavefunction methods for strong correlations of actinides. Our early wavefunction-based approaches focused on extending symmetry-adapted, single-reference coupled cluster for treating strong correlations with feasible computational cost. While we have had some success along these lines, we have recently developed spin-projected unrestricted coupled cluster, which is essentially a black-box multi-reference coupled cluster theory that is superior to unrestricted coupled cluster for small- to medium-sized systems across practically all physical correlation strengths, yet preserves good quantum numbers. For actinides, however, where spin-orbit coupling is often nonnegligible, spin is no longer a fundamental symmetry. We thus propose to develop time reversal and point group projected coupled cluster, which will preserve the fundamental symmetries for actinides. Time reversal projection is achieved via the product of half-spin projection, or spin flip, and complex conjugation projection. Along with point group, these are discrete symmetries, i.e. non-continuous quantum numbers, which, in addition to being the correct symmetries for actinides, can be implemented in lower computational cost than full spin projection. We propose the development of these theories within a synergistic collaboration to use the new methods to elucidate difficult actinide chemistry.

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

Monolayer TiS 2 Nanosheets on Au(111)–Structural Characterization and Effect of Edge Stability for Shape Control

Transition metal dichalcogenides are promising alternatives to noble metal catalysts, e.g., for (photo-)activation of greenhouse gases or hydrogenations. Herein, a direct synthetic route for 2D TiS 2 nanosheets on Au(111) by titanium deposition in the presence of a mild, organic, non-oxidizing sulfur source is presented. High-resolution scanning tunneling microscopy (STM) is used to gain atomic-level insights into the TiS 2 nanosheet morphology. In contrast to the literature, this protocol gains mostly hexagonal and truncated triangular nanosheets with an increased edge contrast in STM, analog to metallic edge states in MoS 2 . Synchrotron-based photoelectron spectroscopy allows insights into compositional details, specifically to distinguish different S sites on the TiS 2 sheets and other S species on the sample. Further, a minimum size is identified (9 S atoms side length), which underlines the importance of moiré reconstructions for stress relief. The TiS 2 sheets coexist with [Au]Ti 1 S 3 clusters, in which a single gold atom is alloyed into the surface and capped by three S atoms. Together with the finding of a critical sheet size, this points toward on-surface Ostwald ripening as a relevant process in the sheet formation. Ab-initio calculations (density functional theory) underscore that the chemical potential of S is an essential descriptor to maintain shape control.

2D nanomaterials↗
DOE OSTI2021

Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Tetracopper σ‐Bound μ ‐Acetylide and ‐Diyne Units Stabilized by a Naphthyridine‐based Dinucleating Ligand

Abstract Reactions of a dicopper(I) tert ‐butoxide complex with alkynes possessing boryl or silyl capping groups resulted in formation of unprecedented tetracopper(I) μ ‐acetylide/diyne complexes that were characterized by NMR and UV/Vis spectroscopy, mass spectrometry and single‐crystal X‐ray diffraction. These compounds possess an unusual μ 4 ‐ η 1 : η 1 : η 1 : η 1 coordination mode for the bridging organic fragment, enforced by the rigid and dinucleating nature of the ligand utilized. Thus, the central π system remains unperturbed and accessible for subsequent reactivity and modification. This has been corroborated by addition of a fifth copper atom, giving rise to a pentacopper acetylide complex. This work may provide a new approach by which metal‐metal cooperativity can be exploited in the transformation of acetylide and diyne groups to a variety of substrates, or as a starting point for the controlled synthesis of copper(I) alkyne‐containing clusters.

Ríos, Pablo↗