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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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Peatland Acidobacteria with a dissimilatory sulfur metabolism
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite ( dsrAB , dsrC , dsrD , dsrN , dsrT , dsrMKJOP ) or sulfate respiration ( sat , aprBA , qmo ABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus . Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering
Abstract The non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip) 2 ] 2+ photosensitizer, where bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kα and Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278 fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered ( 3 MC) excited state surface. This 3 MC state is populated with a 110 fs time constant by 40% of the excited molecules while the rest relax to a 3 MLCT excited state. The sensitivity of the Kα XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1 s and 2p core-ionized states surfaces.
Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning
Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
Mesoscale atomic engineering in a crystal lattice
Controlling individual atoms using lasers, ion traps and scanning probe tips has transformed our understanding of matter and enabled breakthroughs in quantum science. Extending this control into three-dimensional (3D) solids and across mesoscopic scales, however, remains a foundational challenge. Electron irradiation in electron microscopes is known to induce atomic displacements, and atomic manipulation has been proposed and demonstrated. Yet repeated and deterministic control has remained elusive. Here, in this study, we demonstrate deterministic atomic engineering in a 3D crystal, creating ordered arrangements of more than 40,000 user-defined defects within minutes across a 150 nm × 100 nm × 13 nm volume. By steering individual Cr atoms in the magnetic semiconductor CrSBr into selected interstitial sites using an electron beam directed with sub-20-pm-scale accuracy, we create vacancy–interstitial complexes. The resulting impurity array forms a mesoscale crystal embedded within the host lattice, a new form of engineered artificial matter that remains stable at room temperature and outside the microscope. By tracking Cr atom displacements, we identify conditions under which the defect structures are predictable. Our calculations suggest that these defects form correlated impurity states with intra-defect optical transitions and inter-defect kinetic and Coulomb interactions. This establishes a generalizable platform for atomic defect engineering at mesoscopic, and potentially macroscopic, scales, opening opportunities for scalable quantum technologies, including deterministic colour-centre placement, quantum simulation of many-body lattice models and atomic-scale manufacturing.
Large electromechanical strain and unconventional domain switching near phase convergence in a Pb-free ferroelectric
In many ferroelectrics, large electromechanical strains are observed near regions of composition- or temperature- driven phase coexistence. Phenomenologically, this is attributed to easy re-orientation of the polarization vector and/or phase transition, although their effects are highly convoluted and difficult to distinguish experimentally. Here, we used synchrotron X-ray scattering and digital image correlation to differentiate between the microscopic mechanisms leading to large electrostrains in an exemplary Pb-free piezoceramic Sn-doped barium calcium zirconate titanate. Large electrostrains of ~0.2% measured at room-temperature are attributed to an unconventional effect, wherein polarization switching is aided by a reversible phase transition near the tetragonal-orthorhombic phase boundary. Additionally, electrostrains of ~0.1% or more could be maintained from room temperature to 140°C due to a succession of different microscopic mechanisms. In situ X-ray diffraction elucidates that while 90° domain reorientation is pertinent below the Curie temperature ( T C ), isotropic distortion of polar clusters is the dominant mechanism above T C .
Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2'-bipyridine)(CN) 4 ] 2-
The excited state dynamics of solvated [Fe(bpy)(CN) 4 ] 2- , where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN) 4 ] 2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile. Here, in the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN) 4 ] 2- in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet ( 3 MC) character, unlike other reported six-coordinate Fe(II)-centered coordination compounds, which form MC quintet ( 5 MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN) 4 ] 2- allows us to infer the influence of the solvent on the electronic structure of the complex. Lastly, the robust characterization of the dynamics and optical spectral signatures of the isolated 3 MC intermediate provides a strong foundation for identifying 3 MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.
Finding intersections between electronic excited state potential energy surfaces with simultaneous ultrafast X-ray scattering and spectroscopy
Combined X-ray free-electron laser techniques pinpoints loci of intersections between potential energy surfaces of a photo-excited 3d transition-metal centered molecule.
Cubes on a string: a series of linear coordination polymers with cubane-like nodes and dicarboxylate
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A mechanism for ageing in a deeply supercooled molecular glass
Measurements of the decay of electric fields, formed spontaneously within vapour-deposited films of cis-methyl formate, provide the first direct assessment of the energy barrier to secondary relaxation in a molecular glass. At temperatures far below the glass transition temperature, the mechanism of relaxation is shown to be through hindered molecular rotation. Magnetically-polarised neutron scattering experiments exclude diffusion, which is demonstrated to take place only close to the glass transition temperature.
Low temperature aging in a molecular glass: the case of cis -methyl formate
Glassy films of cis-methyl formate show spontaneous dipole orientation on deposition from the vacuum, the so-called ‘spontelectric effect’, creating surface potentials and electric fields within the films. We follow the decay of these fields, and their accompanying dipole orientation, on the hours timescale at deposition temperatures between 40 K and 55 K. Our data trace the low temperature ‘secondary decay’ mechanism, at tens of degrees below the glass transition temperature of 90 K. We show that secondary decay is due to molecular rotation, with associated activation energies lying between 0.1 and 0.2 eV. Diffusion is absent, as established from published neutron reflectivity data. Using an analytical model for the spontelectric effect, data are placed on a quantitative footing, showing that angular motion in excess of 50° reproduces the observed values of activation energies. Exploitation of the spontelectric effect is new in the study of glass aging and is shown here to give insight into the elusive processes which take place far from the molecular glass transition temperature.
Charges on a suspended silicon nitride membrane under a high-energy electron beam
Thin silicon nitride (SiN x ) membranes are widely used in gas and liquid phase transmission electron microscopy (TEM) and as phase plates to enhance imaging contrast. SiN x contains trap sites for both positive and negative charges, which can be manipulated by high-energy electron irradiation, external potential biasing, or light exposure. Charge accumulation on the membrane can significantly affect in situ TEM processes, including chemical and electrochemical reactions, nanoparticle dynamics, and catalytic activity, or introduce unwanted phase shifts when used as a phase plate. Here, in this study, charge accumulation on suspended SiN x membranes was investigated using off-axis electron holography combined with model-free charge analysis, supported by custom finite element analysis (FEA) simulations. An average residual positive charge density of approximately 2.8 × 10 −4 C m −2 was measured. Localized and stable regions of both positive and negative charges were identified on the membrane. The global positive and localized positive/negative charges give rise to strong electric fields and electroosmotic slip velocities at the membrane surface, which are sufficient to induce non-Brownian particle behavior and directional fluid flow, offering a physical explanation for previously observed anomalies in particle dynamics, nucleation, and growth during gas and liquid phase TEM experiments. These results provide a benchmark for understanding charge behavior at SiNx interfaces in gas and liquid phase TEM. Furthermore, the FEA simulations establish a framework for future investigations into charge distribution, electrostatic potentials, and electrical double layers at solid–liquid interfaces, particularly in complex geometries and chemically dynamic environments.
Growth direction of oblique angle electron beam deposited silicon monoxide thin films identified by optical second-harmonic generation
Oblique angle deposited (OAD) silicon monoxide (SiO) thin films forming tilted columnar structures have been characterized by second-harmonic generation. It was found that OAD SiO leads to a rotationally anisotropic second-harmonic response, depending on the optical angle of incidence. A model for the observed dependence of the second-harmonic signal on optical angle of incidence allows extraction of the growth direction of OAD films. The optically determined growth directions show convincing agreement with cross-sectional scanning electron microscopy images. In addition to a powerful characterization tool, these results demonstrate the possibilities for designing nonlinear optical devices through SiO OAD.
Comment on “Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set” [J. Chem. Phys. 139, 114104 (2013)]
In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, and that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.
Revealing origin of quasi-one dimensional current transport in defect rich two dimensional materials
The presence of defects in graphene have for a long time been recognized as a bottleneck for its utilization in electronic and mechanical devices. We recently showed that micro four-point probes may be used to evaluate if a graphene film is truly 2D or if defects in proximity of the probe will lead to a non-uniform current flow characteristic of lower dimensionality. In this work, simulations based on a finite element method together with a Monte Carlo approach are used to establish the transition from 2D to quasi-1D current transport, when applying a micro four-point probe to measure on 2D conductors with an increasing amount of line-shaped defects. Clear 2D and 1D signatures are observed at low and high defect densities, respectively, and current density plots reveal the presence of current channels or branches in defect configurations yielding 1D current transport. A strong correlation is found between the density filling factor and the simulation yield, the fraction of cases with 1D transport and the mean sheet conductance. The upper transition limit is shown to agree with the percolation threshold for sticks. Finally, the conductance of a square sample evaluated with macroscopic edge contacts is compared to the micro four-point probe conductance measurements and we find that the micro four-point probe tends to measure a slightly higher conductance in samples containing defects.
VESPA: The vibrational spectrometer for the European Spallation Source
VESPA, Vibrational Excitation Spectrometer with Pyrolytic-graphite Analysers, aims to probe molecular excitations via inelastic neutron scattering. It is a thermal high resolution inverted geometry time-of-flight instrument designed to maximise the use of the long pulse of the European Spallation Source. The wavelength frame multiplication technique was applied to provide simultaneously a broad dynamic range (about 0-500 meV) while a system of optical blind choppers allows to trade flux for energy resolution. Thanks to its high flux, VESPA will allow the investigation of dynamical and in situ experiments in physical chemistry. Here we describe the design parameters and the corresponding McStas simulations.