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At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗
DOE OSTI2015

The formation and structure of mechano-synthesized nanocrystalline Sr{sub 3}Fe{sub 2}O{sub 6.4}: XRD Rietveld, Mössabuer and XPS analyses

Highlights: • The formation of mechano-synthesized nanocrystalline Sr{sub 3}Fe{sub 2}O{sub 7−δ} is investigated. • Pre-milling the reactants substantially lowers the formation temperature. • The core and surface structures were studied. • XRD and {sup 57}Fe Mössbauer spectroscopic analyses indicate the δ-value to be 0.60. • XPS shows a complex surface structure for the mechanosynthesized Sr{sub 3}Fe{sub 2}O{sub 7−δ} nanoparticles. - Abstract: The influence of ball milling and subsequent sintering of a 3:1 molar mixture of SrCO{sub 3} and α-Fe{sub 2}O{sub 3} on the formation of Sr{sub 3}Fe{sub 2}O{sub 7−δ} double perovskite is investigated with different analytical techniques. Milling the mixture for 110 h leads to the formation of SrCO{sub 3}-α-Fe{sub 2}O{sub 3} nanocomposites and the structural deformation of α-Fe{sub 2}O{sub 3} via the incorporation of Sr{sup 2+} ions. Subsequent sintering of the pre-milled reactants’ mixture has led to the partial formation of an SrFeO{sub 3} perovskite-related phase in the temperature range 400–600 °C. This was followed by the progressive development of an Sr{sub 3}Fe{sub 2}O{sub 7−δ} phase that continued to increase with increasing sintering temperature until a single-phased nanocrystalline Sr{sub 3}Fe{sub 2}O{sub 7−δ} phase was attained at 950 °C (12 h). This temperature is ∼350 °C lower than the temperature at which the material is prepared conventionally using the ceramic method. The evolution of different structural phases during the reaction process is discussed. Rietveld refinement of the X-ray diffraction data shows a value of 0.60 for the oxygen deficiency δ, in consistency with the Fe{sup 3+}/Fe{sup 4+} ratio derived from the {sup 57}Fe Mössbauer data recorded at both 300 K and 78 K. The Mössbauer data suggests that the Sr{sub 3}Fe{sub 2}O{sub 6.4} nanoparticles are superparamagnetic with blocking temperatures below 78 K. The surfaces of the Sr{sub 3}Fe{sub 2}O{sub 6.4} nanoparticles were shown to have a complex structure and composition relative to those of their cores with traces of SrCO{sub 3}, SrO and SrFeO{sub 3−δ} being detected.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

ODIN: Characterizing the Three-dimensional Structure of Two Protocluster Complexes at z = 3.1

We present a detailed study of the 3D morphology of two extended associations of multiple protoclusters at z = 3.1. These protocluster "complexes," designated COSMOS-z3.1-A and COSMOS-z3.1-C, are the most prominent overdensities of z = 3.1 Lyα emitters (LAEs) identified in the COSMOS field by the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey. These protocluster complexes have been followed up with extensive spectroscopy from Keck, Gemini, and DESI. Using a probabilistic method that combines photometrically selected and spectroscopically confirmed LAEs, we reconstruct the 3D structure of these complexes on scales of ≈50 cMpc. We validate our reconstruction method using the IllustrisTNG300-1 cosmological hydrodynamical simulation and show that it consistently outperforms approaches relying solely on spectroscopic data. The resulting 3D maps reveal that both complexes are irregular and elongated along a single axis, emphasizing the impact of sightline on our perception of structure morphology. The complexes consist of multiple density peaks, 10 in COSMOS-z3.1-A and 4 in COSMOS-z3.1-C. The former is confirmed to be a proto-supercluster, similar to Hyperion at z = 2.4 but observed at an even earlier epoch. Multiple "tails" connected to the cores of the density peaks are seen, likely representing cosmic filaments feeding into these extremely overdense regions. The 3D reconstructions further provide strong evidence that Lyα blobs preferentially reside in the outskirts of the highest density regions. Descendant mass estimates of the density peaks suggest that COSMOS-z3.1-A and COSMOS-z3.1-C will evolve to become ultramassive structures by z = 0, with total masses log ( M / M ,⊙ ,) ≳ 15.3 , exceeding that of Coma.

Ramakrishnan, Vandana [Purdue U., West Lafayette] ↗
DOE OSTI2022

Chemical Pressure-Derived Assembly Principles for Dodecagonal Quasicrystal Approximants and Other Complex Frank–Kasper Phases

The structures of complex intermetallic compounds can often be interpreted in terms of assemblies of units from simpler parent phases. For example, dodecagonal quasicrystals appear, when viewed down their high-symmetry axes, as plane-filling arrangements of square and triangular tiles corresponding to the Cr 3 Si and Al 3 Zr 4 structure types, respectively. The atomic arrangements and cell-dimensions at the (100) faces of the cells of these structures provide a close geometrical match, which underlies not only dodecagonal quasicrystals and their approximants, but also the much more common σ-phase structure. In this Article, we show that such intergrowth of parent structures can arise from more than just geometrical coincidences, but can be driven by a complementary matching of atomic packing forces. DFT-Chemical Pressure (CP) analysis on elemental versions of the Cr 3 Si and Al 3 Zr 4 types reveal that in both cases arrays of positive interatomic pressures inhibit the formation of optimal contacts elsewhere in the structures. When they are lined up at the potential Cr 3 Si/Al 3 Zr 4 interfaces, however, positive pressures from the two structures interdigitate rather than coincide, providing the opportunity for the relaxation of strained interatomic contacts. That such relief is afforded by the interfaces is confirmed by CP analysis of the σ-phase (FeCr-type) structure. Building on this scheme, we introduce the CP interface function to represent how the CP features of atoms within a structure impact planes or other surfaces that could serve as interfaces between different structures. Using this function, we then explore how the favorability of interfaces between Cr 3 Si and Al 3 Zr 4 -type units is tuned by partial elemental substitution with Si, as well as their potential matches with Laves phase units. Furthermore, the emerging picture provides an account for features of the quasicrystal approximants Mn 7 VSi 2 and Mn 81.5 Si 18.5 , as well as a framework for approaching intermetallic intergrowth structures more broadly.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Role of chemically and thermally induced crystal lattice distortion in enhancing the Seebeck coefficient in complex tellurides

Composition and crystal structure of complex materials can significantly change the Seebeck effect, i.e., heat to electrical energy conversion, which is utilized in thermoelectric materials. Despite decades of studies of various thermoelectric materials and their application, the fundamental understanding of this effect still is limited. One of the most efficient groups of thermoelectric materials is based on GeTe, where Ge is replaced by [Ag + Sb], i.e., Ag x Sb x Ge 50-2x Te 50 alloys, traditionally shown as (GeTe) m (AgSbTe 2 ) 100-m (TAGS-m series). Here, in this article, we report on the discovery of two unique phenomena in TAGS materials attributed to the effects from [Ag + Sb] atoms: (i) a linear relation between the Seebeck coefficient and rhombohedral lattice distortion, and (ii) resonance-like temperature-induced behavior of the contribution to the Seebeck coefficient produced by [Ag + Sb] atoms. Finally, our findings show that heat to electrical energy conversion strongly depends on the temperature- and compositionally-induced rhombohedral to cubic transformation where [Ag + Sb] atoms play a crucial mediating role.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Single‐Site Carbon‐Supported Metal‐Oxo Complexes in Heterogeneous Catalysis: Structure, Reactivity, and Mechanism

Abstract When early transition metal complexes are molecularly grafted onto catalyst supports, well‐defined, surface‐bound species are created, which are highly active and selective single‐site heterogeneous catalysts (SSHCs) for diverse chemical transformations. In this minireview, we analyze and summarize a less conventional type of SSHC in which molybdenum dioxo species are grafted onto unusual carbon‐unsaturated scaffolds, such as activated carbon, reduced graphene oxide, and carbon nanohorns. The choice of earth‐abundant, low‐toxicity, versatile metal constituents, and various carbon supports illustrates “catalyst by design” principles and yields insights into new catalytic systems of both academic and technological interest. Here, we summarize experimental and computational investigations of the bonding, electronic structure, reaction scope, and mechanistic pathways of these unusual catalysts.

Liu, Yiqi↗
DOE OSTI2014

Spatially adaptive stochastic methods for fluid–structure interactions subject to thermal fluctuations in domains with complex geometries

We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid–structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation–dissipation balance condition to develop compatible stochastic driving fields for our discretization. We perform analysis that shows our condition is sufficient to ensure results consistent with statistical mechanics. We show the Gibbs–Boltzmann distribution is invariant under the stochastic dynamics of the semi-discretization. To generate efficiently the required stochastic driving fields, we develop a Gibbs sampler based on iterative methods and multigrid to generate fields with O(N) computational complexity. Our stochastic methods provide an alternative to uniform discretizations on periodic domains that rely on Fast Fourier Transforms. To demonstrate in practice our stochastic computational methods, we investigate within channel geometries having internal obstacles and no-slip walls how the mobility/diffusivity of particles depends on location. Our methods extend the applicability of fluctuating hydrodynamic approaches by allowing for spatially adaptive resolution of the mechanics and for domains that have complex geometries relevant in many applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Structure and Bonding Investigation of Plutonium Peroxocarbonate Complexes Using Cerium Surrogates and Electronic Structure Modeling

Herein, we report the synthesis and structural characterization of K8[(CO3)3Pu]2(µ-η2-η2-O2)2•12H2O. This is the second plutonium-containing addition to the previously studied alkali metal peroxo-carbonate series M8[(CO3)3A]2(µ-η2-η2-O2)2•xH2O (M = alkali metal; A = Ce or Pu; x = 8, 10, 12 or 18), for which only the M = Na analog has been previously reported when A = Pu. The previously reported crystal structure for Na8[(CO3)3Pu]2(µ-η2-η2-O2)2•12H2O is not isomorphous with its known Ce analogue. However, a new synthetic route to these M8[(CO3)3A]2(µ-η2-η2-O2)2•12H2O complexes, described below, has produced crystals of Na8[(CO3)3Ce]2(µ-η2-η2-O2)2•12H2O that are isomorphous with the previously reported Pu analogue. Via this synthetic method, the M = Na, K, Rb, and Cs salts of M8[(CO3)3Ce]2(µ-η2-η2-O2)2•xH2O have also been synthesized for systematic structural comparison with each other and the available Pu analogues using single-crystal X-ray diffraction, Raman spectroscopy and density functional theory (DFT) calculations. The cerium salts in particular demonstrate subtle differences in the peroxide bond lengths which correlate to Raman shifts for the peroxide Op–Op stretch (Op = the oxygen atoms of the peroxide bridges) with each of the cations studied: Na+ (1.492(3) Å /847 cm-1), Rb+ (1.471(1) Å /854 cm-1), Cs+ (1.474(1) Å /859 cm-1), and K+ (1.468(6) Å, 870 cm-1). The trends observed in the M–Op and Op–Op bond distances appear to relate to supermolecular interactions between the neighboring cations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Understanding the Electronic Structure of 4d Metal Complexes: From Molecular Spinors to L-Edge Spectra of a di-Ru Catalyst

L{sub 2,3}-edge X-ray absorption spectroscopy (XAS) has demonstrated unique capabilities for the analysis of the electronic structure of di-Ru complexes such as the blue dimer cis,cis-[Ru{sub 2}{sup III}O(H{sub 2}O){sub 2}(bpy){sub 4}]{sup 4+} water oxidation catalyst. Spectra of the blue dimer and the monomeric [Ru(NH{sub 3}){sub 6}]{sup 3+} model complex show considerably different splitting of the Ru L{sub 2,3} absorption edge, which reflects changes in the relative energies of the Ru 4d orbitals caused by hybridization with a bridging ligand and spin-orbit coupling effects. To aid the interpretation of spectroscopic data, we developed a new approach, which computes L{sub 2,3}-edges XAS spectra as dipole transitions between molecular spinors of 4d transition metal complexes. This allows for careful inclusion of the spin-orbit coupling effects and the hybridization of the Ru 4d and ligand orbitals. The obtained theoretical Ru L{sub 2,3}-edge spectra are in close agreement with experiment. Critically, existing single-electron methods (FEFF, FDMNES) broadly used to simulate XAS could not reproduce the experimental Ru L-edge spectra for the [Ru(NH{sub 3}){sub 6}]{sup 3+} model complex nor for the blue dimer, while charge transfer multiplet (CTM) calculations were not applicable due to the complexity and low symmetry of the blue dimer water oxidation catalyst. We demonstrated that L-edge spectroscopy is informative for analysis of bridging metal complexes. The developed computational approach enhances L-edge spectroscopy as a tool for analysis of the electronic structures of complexes, materials, catalysts, and reactive intermediates with 4d transition metals.

Alperovich, Igor↗
DOE OSTI2014

Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Geometric and electronic structures of potassium-adsorbed rubrene complexes

The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments than the other two on the opposite side, which leads to the largely enhanced resemblance of the simulated to the experimental spectra. Fourth, the HOMO and LUMO are mainly the α and β components of the 2p orbitals of the backbone carbons, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks

Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. To illuminate these forces, we determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked β sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. By computationally threading the human proteome on our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such interactions. Finally, these segments are found in proteins as diverse as RNA binders, nuclear pore proteins, and keratins, which are known to form networks and localize to membraneless assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Structural hierarchy as a key to complex phase selection in Al-Sm

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and split Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60 Sm 11 (bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60 Sm 11 (bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.

36 MATERIALS SCIENCE↗