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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Shape-driven, emergent behavior in active particle mixtures

Abstract Active particle systems can vary greatly from one-component systems of spheres to mixtures of particle shapes at different composition ratios. We investigate computationally the combined effect of anisotropy and stoichiometry on the collective behavior of two-dimensional active colloidal mixtures of polygons. We uncover three emergent phenomena not yet reported in active Brownian particle systems. First, we find that mixtures containing hexagons exhibit micro-phase separation with large grains of hexagonal symmetry. We quantify a measurable, implicit ‘steric attraction’ between the active particles as a result of shape anisotropy and activity. This calculation provides further evidence that implicit interactions in active systems, even without explicit attraction, can lead to an effective preferential attraction between particles. Next, we report stable fluid clusters in mixtures containing one triangle or square component. We attribute the fluidization of the dense cluster to the interplay of cluster destabilizing particles, which introduce grain boundaries and slip planes into the system, causing solid-like clusters to break up into fluid clusters. Third, we show that fluid clusters can coexist with solid clusters within a sparse gas of particles in a steady state of three coexisting phases. Our results highlight the potential for a wide variety of behavior to be accessible to active matter systems and establish a route to control active colloidal systems through simple parameter designs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Photoelectron spectroscopy of CsK2Sb photocathode at Synchrotron Radiation Facility using vacuum transport system

As accelerators and electron microscopes become more advanced, high-performance photocathodes are required. In particular, Cesium potassium antimonide (CsK 2 Sb) photocathode is of interest because of its low emittance, excitability in visible light, and high quantum efficiency (QE). The challenge is its high susceptibility to environment that lead to low operating vacuum pressure and short lifetime/low extraction charge. To resolve these issues, it is necessary to understand the molecular structure of the cathode and its degradation mechanism. In this study, we transported CsK 2 Sb photocathode to a beamline of synchrotron radiation facility using a vacuum transport system for molecular structure analysis. Specifically, the cathode was deposited in an evaporation system at Nagoya University. We transported it to Aichi Synchrotron Radiation Center (Aichi SR) located 15 km away, and analyzed it in the depth direction by X-ray photoelectron spectroscopy (XPS) at BL7U. Based on the results, we quantitatively evaluated the composition ratios and stoichiometry of the cathode elements (Sb, K, Cs). A Cs ex-cess state of surface was observed at the surface, and it is consistent with previous studies. The intended atomic structure of CsK 2 Sb was formed only at a few nanometres of the surface on the Mo substrate. On the other hand, the CsK 2 Sb cathode structure on the graphene substrate was preserved further in the depth direction.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Shifts in valence states in bimetallic MXenes revealed by electron energy-loss spectroscopy (EELS)

MXenes are an emergent class of two-dimensional materials with a very wide spectrum of promising applications. The synthesis of multiple MXenes, specifically solid-solution MXenes, allows fine tuning of their properties, expands their range of applications, and leads to enhanced performance. The functionality of solid-solution MXenes is closely related to the valence state of their constituents: transition metals, oxygen, carbon, and nitrogen. However, the impact of changes in the oxidation state of elements in MXenes is not well understood. In this work, three interrelated solid-solution MXene systems (Ti$_{2–y}$Nb$_y$CT$_x$, Nb$_{2–y}$V$_y$CT$_x$, and Ti$_{2–y}$V$_y$CT$_x$) were investigated with scanning transmission electron microscopy and electron energy-loss spectroscopy to determine the localized valence states of metals at the nanoscale. The analysis demonstrates changes in the electronic configuration of V upon modification of the overall composition and within individual MXene flakes. These shifts of oxidation state can explain the nonlinear optical and electronic features of solid-solution MXenes. Vanadium appears to be particularly sensitive to modification of the valence state, while titanium maintains the same oxidation state in Ti–Nb and Ti–V MXenes, regardless of stoichiometry. Here, the study also explains Nb's influential role in the previously observed electronic properties in the Nb–V and Nb–Ti systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Stoichiometric Ecotoxicology for a Multisubstance World

Nutritional and contaminant stressors influence organismal physiology, trophic interactions, community structure, and ecosystem-level processes; however, the interactions between toxicity and elemental imbalance in food resources have been examined in only a few ecotoxicity studies. Integrating well-developed ecological theories that cross all levels of biological organization can enhance our understanding of ecotoxicology. In the present article, we underline the opportunity to couple concepts and approaches used in the theory of ecological stoichiometry (ES) to ask ecotoxicological questions and introduce stoichiometric ecotoxicology, a subfield in ecology that examines how contaminant stress, nutrient supply, and elemental constraints interact throughout all levels of biological organization. This conceptual framework unifying ecotoxicology with ES offers potential for both empirical and theoretical studies to deepen our mechanistic understanding of the adverse outcomes of chemicals across ecological scales and improve the predictive powers of ecotoxicology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410–DNA interaction using small angle X-ray scattering

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene

Abstract Left-handed G-quadruplexes (LHG4s) belong to a class of recently discovered noncanonical DNA structures under the larger umbrella of G-quadruplex DNAs (G4s). The biological relevance of these structures and their ability to be targeted with classical G4 ligands is underexplored. Here, we explore whether the putative LHG4 DNA sequence from the SLC2A1 oncogene promoter maintains its left-handed characteristics upon addition of nucleotides in the 5′- and 3′-direction from its genomic context. We also investigate whether this sequence interacts with a well-established G4 binder, N-methylmesoporphyrin IX (NMM). We employed biophysical and X-ray structural studies to address these questions. Our results indicate that the sequence d[G(TGG)3TGA(TGG)4] (termed here as SLC) adopts a two-subunit, four-tetrad hybrid left-/right-handed G4 (LH/RHG4) topology. Addition of 5′-G or 5′-GG abolishes the left-handed fold in one subunit, while the addition of 3′-C or 3′-CA maintains the original fold. X-ray crystal structure analyses show that SLC maintains the same hybrid LH/RHG4 fold in the solid state and that NMM stacks onto the right-handed subunit of SLC. NMM binds to SLC with a 1:1 stoichiometry and a moderate-to-tight binding constant of 15 μM−1. This work deepens our understanding of LHG4 structures and their binding with traditional G4 ligands.

Seth, Paul↗
DOE OSTI2021

Inactivation of mitochondrial complex I stimulates chloroplast ATPase in Physcomitrium patens

Abstract Light is the ultimate source of energy for photosynthetic organisms, but respiration is fundamental for supporting metabolism during the night or in heterotrophic tissues. In this work, we isolated Physcomitrella (Physcomitrium patens) plants with altered respiration by inactivating Complex I (CI) of the mitochondrial electron transport chain by independently targeting on two essential subunits. Inactivation of CI caused a strong growth impairment even in fully autotrophic conditions in tissues where all cells are photosynthetically active, demonstrating that respiration is essential for photosynthesis. CI mutants showed alterations in the stoichiometry of respiratory complexes while the composition of photosynthetic apparatus was substantially unaffected. CI mutants showed altered photosynthesis with high activity of both Photosystems I and II, likely the result of high chloroplast ATPase activity that led to smaller ΔpH formation across thylakoid membranes, decreasing photosynthetic control on cytochrome b6f in CI mutants. These results demonstrate that alteration of respiratory activity directly impacts photosynthesis in P. patens and that metabolic interaction between organelles is essential in their ability to use light energy for growth.

Plant Sciences↗
DOE OSTI2025

PII interactions with the acetyl-CoA carboxylase subunits BADC and BCCP co-regulate lipid and nitrogen metabolism in Arabidopsis

In plants, the initiation of fatty acid synthesis is catalyzed by acetyl-CoA carboxylase (ACCase), which produces malonyl-CoA. The heteromeric form of ACCase (htACCase) is a holoenzyme consisting of biotin carboxylase and carboxyltransferase sub-complexes, both of which are subject to extensive regulation. Biotin carboxylase activity is controlled in part by the presence of the catalytic biotin carboxyl carrier proteins (BCCP1/2) and/or the non-catalytic, non-biotinylated, biotin/lipoyl attachment domain-containing proteins (BADC1/2/3) that associate with backbone biotin carboxylase (BC) protein. However, the mechanisms regulating BADC and BCCP interactions with BC and, consequently, ACCase activity in planta , remain unclear. Here, we demonstrate that the Arabidopsis ( Arabidopsis thaliana ) regulatory protein PII modulates htACCase activity through independent interactions with BADC and BCCP proteins in a selective manner. Analysis of badc1 badc2 and badc1 badc3 mutant lines and the respective pii triple mutants revealed that changes in seed oil and protein accumulation of badc double mutants are PII/nitrogen dependent. Absolute quantification of htACCase subunits and PII in developing seeds suggests that Arabidopsis exerts tight regulation over individual protein stoichiometry to balance oil and protein accumulation. The effects on vegetative and seed development indicate that PII and BADC proteins have distinct yet overlapping roles in regulating plant metabolism.

Garneau, Matthew G. [Washington State Univ., Pullm↗
DOE OSTI2024

50 Years of metabolic control analysis

It has been 50 years since the publication of the seminal works by Savageau, Kacser & Burns and Heinrich & Rapoport, on the control of biochemical networks. What is remarkable about these three publications (especially the two papers by Kacser et al. and Rapoport et al.) is that they independently developed almost the same approach and came to the same conclusions. This approach is today called metabolic control analysis (MCA), and is a body of work that uses mathematics to reason about the properties of biochemical pathways in a deductive manner. Although originally focused on metabolic pathways, it was realized early on that it could be equally applied to genetic and signalling networks. In fact anything that one could associate a stoichiometry matrix with. In recent years, others have reinvented MCA, using different notation, highlighting the fact that there has been a good deal of conceptual convergence in this area.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular mechanism for the interaction between human CPSF30 and hFip1

Most eukaryotic pre-mRNAs must undergo 3'-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3'-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2–ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4–ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4–ZF5 in complex with residues 161–200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30–hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a K d of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30–hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Electronic Structure of Compressively Strained Bilayer Nickelate Thin Film

The discovery of superconductivity in bulk bilayer nickelates under high pressure, and its subsequent stabilization in compressively strained thin films at ambient pressure, has established a new platform for exploring high-𝑇 c superconductivity beyond the cuprates. Central to this development is the prominent role of the 3⁢𝑑$^2_𝑧$ orbital in shaping the low-energy electronic structure, imposing constraints on microscopic theories and fueling debate over the superconducting mechanism. Here we report a systematic in situ angle-resolved photoemission spectroscopy study of compressively strained bilayer nickelate thin films spanning Ca doping, oxygen stoichiometry and film thickness. Despite variations in oxygen-vacancy disorder and surface termination, the electronic structure remains robust and exhibits a systematic strain-driven evolution consistent with an intermediate-correlation regime. In particular, we demonstrate a Ca-doping-induced electronic structure evolution that is consistent with Fermi-level crossing of the 𝛾 band and is decoupled from the presence of superconductivity, suggesting that, while important for the 𝛾 band to be near the Fermi level, the debated 𝛾 crossing and the resulting Fermi pocket may not be a prerequisite for superconductivity. Together, our results establish key spectroscopic constraints on the minimal fermiology and correlation strength relevant to superconductivity in bilayer nickelates, providing an experimental foundation for microscopic theories of their pairing mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Electronic Origin of Delicate Antiferromagnetism in Fe 𝑥 ⁢NbS 2

Among the family of intercalated transition-metal dichalcogenides (TMDs), Fe 𝑥 ⁢NbS 2 is found to possess unique current-induced resistive switching behaviors, tunable antiferromagnetic states, and a commensurate charge order, all of which are tied to a critical Fe doping of 𝑥 𝑐 = 1/3. However, the electronic origin of such extreme stoichiometry sensitivities remains unclear. Combining angle-resolved photoemission spectroscopy (ARPES) with density functional theory (DFT) calculations, we identify and characterize a dramatic eV-scale electronic restructuring that occurs across the 𝑥𝑐. Moment-carrying Fe 3⁢𝑑 𝑧 2 electrons manifest as narrow bands within 200 meV of the Fermi level, distinct from other transition metal intercalated TMD magnets. These states strongly hybridize with itinerant electrons in the TMD layer and rapidly lose coherence above 𝑥 𝑐 due to correlation-driven effects. This sudden quasiparticle decoherence collapses the Fe-Nb hybridization, which explicitly suppresses the out-of-plane effective Fe-Fe exchange interaction, driving the transformation of the magnetic ground state from an antiferromagnetic stripe phase to a zigzag phase. Furthermore, these observations resemble the exceptional electronic and magnetic sensitivity of strongly correlated systems, and demonstrate that quantifying orbital-specific hybridization via ARPES offers an alternative pathway to evaluate effective magnetic exchange in metallic magnets, complementing inelastic neutron and resonant x-ray scattering probes.

Angle-resolved photoemission spectroscopy↗
DOE OSTI2025

Evolution of magnetoresistance in the magnetic topological semimetals NdS⁢b 𝑥⁢ T⁢e 2−𝑥

Magnetic topological semimetals 𝐿𝑛⁢SbTe (𝐿𝑛=lanthanide elements) provide a platform to study the interplay of structure, magnetism, topology, and electron correlations. Varying Sb and Te compositions in 𝐿⁢𝑛⁢S⁢b 𝑥 ⁢T⁢e 2−𝑥 can effectively control the electronic, magnetic, and transport properties. Here, we report the evolution of transport properties with Sb and Te contents in NdS⁢b 𝑥 ⁢T⁢e 2−𝑥 , (0<𝑥<1). Our work reveals nonmonotonic evolution in magnetoresistance with varying composition stoichiometry. Specifically, reducing Sb content 𝑥 leads to strong negative magnetoresistance up to 99.9%. Such a strong magnetoresistance, which is likely attributed to the interplay between structure, magnetism, and electronic bands, establishes this material as a promising platform for investigating topological semimetal for future device applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Structural modulation, physical properties, and electronic band structure of the kagome metal UCr 6 ⁢Ge 6

The chemical flexibility of the 𝑅⁢𝑀 6 ⁢𝑋 6 stoichiometry, where an 𝑓-block element is intercalated in the CoSn structure type, allows for the tuning of flatbands associated with kagome lattices to the Fermi level and for emergent phenomena due to interactions between the 𝑓- and 𝑑-electron lattices. Yet, 5⁢𝑓 members of the “166” compounds are underrepresented compared with 4⁢𝑓 members. In this work, we report single-crystal growth of UCr 6 ⁢Ge 6 , which crystallizes in a monoclinically distorted Y 0.5⁢ Co 3 ⁢Ge 3 -type structure. The real-space character of the modulation, which is unique within the 𝑅⁢𝑀 6 ⁢𝑋 6 family, is approximated by a 3×1×2 supercell of the average monoclinic cell. The compound has kagome-lattice flatbands near the Fermi level and a moderately enhanced electronic heat capacity, as evidenced by its low-temperature Sommerfeld coefficient (𝛾=86.5 mJ mol −1 K −2 ) paired with band structure calculations. The small, isotropic magnetization and featureless resistivity of UCr 6 ⁢Ge 6 suggest itinerant uranium 5⁢𝑓 electrons and Pauli paramagnetism. Angle-resolved photoemission spectroscopy results provide evidence for uranium 5⁢𝑓 weight at the Fermi level and for a flatband near the Fermi level associated with the chromium 3⁢𝑑 kagome lattice. The isotropic magnetic behavior of the uranium 5⁢𝑓 electrons starkly contrasts with localized behavior in other uranium 166 compounds, highlighting the high tunability of the magnetic ground state across the material family.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Route to high-$T_c$ superconductivity via CH 4 -intercalated H 3 S hydride perovskites

While exploring potential superconductors in the C-S-H ternary system using first-principles crystal structure prediction methods, we uncovered a class of hydride perovskites based on the intercalation of methane into an H 3 S framework. These intriguing H 3 S–CH 4 structures emerge as metastable at ~100 GPa. Further, electron-phonon coupling calculations indicate that phases with CSH 7 stoichiometry are potential superconductors with $T_c$ values ranging from 100 K to 190 K at megabar pressures. The results are expected to guide the experimental search for new high-$T_c$ superconductors, including those stable at lower pressures than previously documented superconducting hydrides such as H 3 S and LaH 10 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Enhancing superconductivity of Y 5 Rh 6 Sn 18 by atomic disorder

Here, we investigate the effect of enhancement of superconducting transition temperature $T_c$ by nonmagnetic atom disorder in the filled skutterudite-related tetragonal Y 5 Rh 6 Sn 18 compound doped with Ca. We documented experimentally that Y 5 Rh 6 Sn 18 and its Ca-doped alloys are electronically inhomogeneous at the nanoscale, when Ca content is smaller than ~1.5 in the Y 5– x Ca x Rh 6 Sn 18 system, while for $\textit{x}$ ≥ 1.5 much stronger chemical phase inhomogeneity is observed with an about 20% volume fraction of the second 3:4:13 cubic phase, which we interpret as a fluctuation of stoichiometry within the bulk sample. Then the enhancement of $T_c$ vs $\textit{x}$ could be modeled by a mechanism proposed in recent theoretical reports for increasing the mean-field transition temperature $T_c$ in the presence of nonmagnetic disorder. The increase in disorder with doping increases the sample inhomogeneity and causes a systematic increase in $T_c$, while for two-phase $\textit{x}$ ≥ 1.5 samples the critical temperature $T^{\star}_c ≈ 2 × T_c$ rapidly increases. Based on band structure calculations performed under pressure, we demonstrate how the change in density of states would affect $T_c$ of Y 5 Rh 6 Sn 18 . We obtained the Grüneisen parameter $γ_G$ larger for the inhomogeneous phase with respect to $γ_G$ of the bulk $T_c$ phase and attribute the enhancement of $T_c$ to larger stiffening of the high-temperature $T^{\star}_c$ phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Pressure-induced superconductivity in the hydrogen-rich pseudobinary CaB - H n compounds

Here, the crystal structures of CaB – Hn compounds with n = 1 – 12 in a pressure range of 50–300 GPa were studied using the genetic algorithm method and first-principles density-function theory calculations. Stable structures with stoichiometry of CaB H 6 and CaB H 7 were predicted in different pressure range. BH 4 , BH 5 , and BH 6 units were found to be the main motifs in these compounds. Moreover, metastable Imm2 CaB H 7 is dynamically stable above 180 GPa, with the formation of tetrahedral BH 4 unit surrounded by Ca atom and H 3 unit. Electron-phonon coupling (EPC) calculations reveal that the superconducting properties are closely related to the strong hydrogen-boron bonding of the BH 4 unit in Imm2, and T c can reach ~200 K at 200 GPa. As the major units, BH 4 , BH 5 , and BH 6 units exist in the Imm2, P 2 , and P2 1 /m phases of CaB H 7 at 300 GPa, respectively; the corresponding EPC parameter λ decreases with the increase of hydrogen content in CaB H 7 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗