The sequence–structure–function relationship of intrinsic ERα disorder
Not provided.
Science & Technology - Other Topics↗
SEARCH · Search NASA
Results for “structural disorder”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Correlated Anion Disorder in Heteroanionic Cubic TiOF 2
Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO 3 -type) TiOF 2 using X-ray pair distribution function (PDF), 19 F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF 2 , characterized by predominant cis-[O 2 F 4 ] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19 F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19 F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF 4 . We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ambient and High Pressure CuNiSb 2 : Metal-Ordered and Metal-Disordered NiAs-Type Derivative Pnictides
The mineral Zlatogorite, CuNiSb 2 , was synthesized in the laboratory for the first time by annealing elements at ambient pressure (CuNiSb 2 -AP). Rietveld refinement of synchrotron powder X-ray diffraction data indicates that CuNiSb 2 -AP crystallizes in the NiAs-derived structure ( P 3 m 1, #164) with Cu and Ni ordering. The structure consists of alternate NiSb 6 and CuSb 6 octahedral layers via face-sharing. The formation of such structure instead of metal disordered NiAs-type structure ( P 6 3 / mm c, #194) is validated by the lower energy of the ordered phase by first-principle calculations. Interatomic crystal orbital Hamilton population, electron localization function, and charge density analysis reveal strong Ni-Sb, Cu-Sb, and Cu-Ni bonding and long weak Sb-Sb interactions in CuNiSb 2 -AP. The magnetic measurement indicates that CuNiSb 2 -AP is Pauli paramagnetic. First-principle calculations and experimental electrical resistivity measurements reveal that CuNiSb 2 -AP is a metal. The low Seebeck coefficient and large thermal conductivity suggest that CuNiSb 2 is not a potential thermoelectric material. Single crystals were grown by chemical vapor transport. The high pressure sample (CuNiSb 2 -8 GPa) was prepared by pressing CuNiSb 2 -AP at 700 °C and 8 GPa. However, the structures of single crystal and CuNiSb 2 -8 GPa are best fit with a disordered metal structure in the P 3 m 1 space group, corroborated by transmission electron microscopy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural Color Production in Melanin-Based Disordered Colloidal Nanoparticle Assemblies in Spherical Confinement
Melanin is a ubiquitous natural pigment that exhibits broadband absorption and high refractive index. Despite its widespread use in structural color production, how the absorbing material, melanin, affects the generated color is unknown. Using a combined molecular dynamics and finite-difference time-domain computational approach, here we investigates structural color generation in one-component melanin nanoparticle-based supraparticles (called supraballs) as well as binary mixtures of melanin and silica (nonabsorbing) nanoparticle-based supraballs. Experimentally produced one-component melanin and one-component silica supraballs, with thoroughly characterized primary particle characteristics using neutron scattering, produce reflectance profiles similar to the computational analogs, confirming that the computational approach correctly simulates both absorption and multiple scattering from the self-assembled nanoparticles. These combined approaches demonstrate that melanin's broadband absorption increases the primary reflectance peak wavelength, increases saturation, and decreases lightness factor. Additionally, the dispersity of nanoparticle size more strongly influences the optical properties of supraballs than packing fraction, as evidenced by the production of a larger range of colors when size dispersity is varied versus packing fraction. For binary melanin and silica supraballs, the chemistry-based stratification allows for more diverse color generation and finer saturation tuning than does the degree of mixing/demixing between the two chemistries.
broadband absorption↗
In Situ Scattering Studies of Superconducting Vacancy‐Ordered Monoclinic TiO Thin Films
Abstract The structural and transport properties of vacancy‐ordered monoclinic superconducting titanium oxide (TiO) thin films grown by molecular beam epitaxy are investigated. The evolution of the crystal structure during growth is monitored by in situ synchrotron X‐ray diffraction. Long‐range ordering of Ti and O vacancies in the disordered cubic phase stabilizes the vacancy‐ordered monoclinic TiO phase. The reduced structural disorder arising from vacancy‐ordering is correlated with a superconductor‐metal transition (SMT) in contrast to the superconductor‐insulator transition (SIT) observed in cubic TiO, orthorhombic Ti 2 O 3 , and the Magneli γ − Ti 3 O 5 and γ − Ti 4 O 7 phase. Magnetoresistance measurements for the SIT phases indicate superconducting fluctuations persisting in the normal phase. These results confirm the role of disorder related to Ti and O vacancies and structural inhomogeneity in determining the electronic properties of the normal state of titanium oxide‐based superconductors.
Baksi, Merve↗
X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology
Abstract Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIV BRCT –Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
59 BASIC BIOLOGICAL SCIENCES↗
The structures of mcgovernite and carlfrancisite reconsidered: static disorder or ordered defects and twinning?
Here, the minerals mcgovernite and carlfrancisite possess an extraordinary rhombohedral unit cell [mcgovernite: a = b = 8.206 Å and c = 204.118 Å, with the complex formula unit M 2+ 19 Zn 3 (OH) 21 (AsO 3 )(AsO 4 ) 3 (SiO 4 ) 3 (M = Mn, Mg, Zn); carlfrancisite similar]. Hawthorne [(2018), Mineral. Mag. 82, 1101–1118] reported a single-crystal study using a centrosymmetric model ($R\bar{3}c$) containing disorder on three cationic sites and an AsIII lone-pair site for both mcgovernite and carlfrancisite. A solution of the structure of mcgovernite from high-resolution synchrotron powder diffraction data suggests a reinterpretation of the crystal structures of mcgovernite and carlfrancisite as noncentrosymmetric R3c with ordered planar defects which allows for merohedral twinning.
carlfrancisite↗
The effect of Cu additions in FePt–BN–SiO 2 heat-assisted magnetic recording media
Structural and chemical order impact magnetic properties of solids, which are governed by spin–orbit coupling and exchange interaction. The ordered L1 0 phase of FePt is a key material to heat-assisted magnetic recording; to enable high storage density, a solid understanding is needed of structural and chemical disorder at small length scales, as well as associated modifications of the electronic band structure. Here, we investigate the effect of boron and copper additions (≲6 mol% Cu) on structural and magnetic properties of L1 0 FePt granular media. Two copper-driven mechanisms, although competing, can lead to improvements in both structural and magnetic properties. In particular, the Cu substitution on the Fe-site leads to a degradation of magnetic properties due to the delocalized electron orbitals originating from a larger Cu d -orbital occupancy. At the same time, Cu substitution leads to an enhanced crystallographic order and consequently magneto-crystalline anisotropy, which offsets the former effect to a large extent. Our study is based on magnetometry, x-ray absorption spectroscopy, ab-initio calculations and a phenomenological theory of disordered FePt granular media. We do not observe a sizable modification to Fe moments and electronic configuration; Cu reveals two different resonances associated with the presence and absence of Cu–B bonds that vary with total Cu concentration.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
The hierarchical energy landscape of screw dislocation motion in refractory high-entropy alloys
High-entropy alloys (HEAs) with concentrated solid solutions are conceived to possess a rugged atomic and energy landscape in which dislocation motion necessarily proceeds to accommodate mechanical deformation. Fundamental questions remain as to how rough the energy landscape is and to what extent it can be influenced by the local ordering of their constituent elements. Here, we construct and report the potential energy landscape (PEL) governing screw dislocation motion in refractory HEAs that reveals a hierarchical and multilevel structure with a collection of small basins nested in large metabasin. This striking feature pertaining to HEAs exerts a trapping force and back stress on saddle point activations, retarding dislocation movement. Further, by introducing chemical short-range order, the energy landscape is smoothed but skewed to different degrees that shifts the rate-liming process from kink-glide to kink-pair nucleation. The chemical disorder-roughened PEL in HEAs, analogous to structural disorder induced in metallic glasses, signifies the role of various barrier-hopping processes underlying the extraordinary mechanical behaviors of the two distinct groups of materials.
36 MATERIALS SCIENCE↗
Planar Defect Layers Template a High-Pressure InBi Polymorph
The short- and long-range order of III–V materials under high pressure has long been the subject of debate, with advancements in structural characterization leading to significant revisions to the accepted structural models. Despite these revisions, previous high-pressure structural assignments in the In–Bi system include the site-disordered β-Sn structure type, a structure type demonstrated to be nonexistent in analogous III–V systems. While X-ray diffraction is consistent with site disordering in InBi at high pressure, cluster expansion calculations indicate that disordering requires temperatures above 3000 K. Here, we propose InBi as a model material for studying unique high-pressure planar defects due to its highly anisotropic stress-dependent properties and structure. Specifically, we identify two sets of planar defects that mimic the diffraction pattern of a site disordered β-Sn structure type and are compatible with the calculated disorder barrier. We derive these defects by symmetry relations over crystallographic transitions. Density functional theory calculations of the proposed defects suggest that these defects are stabilized by diminishing interlayer separations with pressure. Further, we find that one of the proposed defects closely resembles a bulk high-pressure phase of InBi, InBi-ϵ, and we assert that the proposed defects order upon heating, acting as a template for InBi-ϵ growth. The proposed defects and their electronic structure provide a basis for the trend of superconducting critical temperature with increasing pressure. These methods for identifying defects are generalizable to other materials with reports of site disorder at high pressure, prompting a broader search for related high-pressure defects.
36 MATERIALS SCIENCE↗
New transformations between crystalline and amorphous ice
High-pressure optical and spectroscopic techniques were used to obtain directly the ice I(h) - hda-ice transformation in a diamond-anvil cell, and the stability of the amorphous form is examined as functions of pressure and temperature. It is demonstrated that hda-ice transforms abruptly at 4 GPa and 77 K to a crystalline phase close in structure to orientationally disordered ice-VII and to a more highly ordered, ice-VIII-like structure at higher temperatures. This is the first time that an amorphous solid is observed to convert to a crystalline solid at low temperatures by compression alone. Phase transitions of this type may be relevant on icy planetary satellites, and there may also be implications for the high-pressure behavior of silica.
Hemley, R. J.↗
Effects of chemical disorder and spin-orbit coupling on the electronic-structure and Fermi-surface topology of YbSb-based monopnictides
Here, in this work, we study the influence of disorder on the electronic structure of YbSb—a rare-earth monopnictide featuring a simple rocksalt (B1) crystal structure and a well-defined Fermi-surface topology—by employing first-principles density-functional theory. We focus on chemical disorder introduced through Te and Al doping, selected based on their thermodynamic stability in alloyed configurations, to understand how such perturbations modify the electronic states of YbSb. Our results indicate that Te doping predominantly introduces electronlike states at the 𝑋 and 𝐿 points, while Al doping leads to a suppression of holelike states at Γ, effectively driving the system from a semimetallic state to one characterized by very narrow-gap behavior at Γ. This modulation of the Fermi surface, particularly the reduction of central hole pockets at Γ, plays a central role in altering interpocket scattering—a mechanism critical for tuning quantum transport properties, including superconductivity. This disorder-driven modulation of the Fermi surface, particularly the suppression of central hole pockets at Γ, controls interpocket scattering, which is essential for optimizing quantum transport properties, including superconductivity. Our results show that disorder can be effectively used for engineering band topology, thereby tuning quantum related response through a tailored electronic structure.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Tuning Cation (Dis)Order in Cr‐Based Li‐Excess Oxide Cathode Materials to Improve Li+ Transport Properties
Abstract Li‐excess disordered rocksalts (DRXs) hold promise as next‐generation cathodes for Li‐ion batteries due to their high capacity and energy density, along with the potential to eliminate the need for Co and Ni. However, due to their low Li + diffusivity, DRXs need to be pulverized into nanoparticles to achieve high performance. Herein, a new strategy for overcoming this limitation is demonstrated, involving the design of as‐synthesized partially disordered oxides with a structure that lies between ordered layered and fully disordered, exhibiting a varying degree of local (dis)order. This unique structure activates new Li + diffusion channels, improving percolation and transport properties. This strategy allows a large content of Li + to be accessed in material with large, micron‐sized particles through highly reversible Cr 3+/6+ and O redox, yielding a first discharge capacity of 286 mAh g −1 (881 Wh kg −1 ). The Li + percolation network is further improved by substituting Ti with a mixture of multiple metals, which appears to locally decrease the migration barrier through lattice distortion. Proper tuning of the chemical composition, especially the content of metals with empty d orbitals, is established as a crucial factor for controlling the degree of disorder and mitigating voltage fade and hysteresis growth upon cycling.
Moździerz, Maciej↗
Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis
Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.
59 BASIC BIOLOGICAL SCIENCES↗
rmc-discord : reverse Monte Carlo refinement of diffuse scattering and correlated disorder from single crystals
A user-friendly program has been developed to analyze diffuse scattering from single crystals with the reverse Monte Carlo method. The approach allows for refinement of correlated disorder from atomistic supercells with magnetic or structural (occupational and/or displacive) disorder. The program is written in Python and optimized for performance and efficiency. Refinements of two user cases obtained with legacy neutron-scattering data demonstrate the effectiveness of the approach and the developed program. It is shown with bixbyite, a naturally occurring magnetic mineral, that the calculated three-dimensional spin-pair correlations are resolved with finer real-space resolution compared with the pair distribution function calculated directly from the reciprocal-space pattern. With the triangular lattice Ba 3 Co 2 O 6 (CO 3 ) 0.7 , refinements of occupational and displacive disorder are combined to extract the one-dimensional intra-chain correlations of carbonate molecules that move toward neighboring vacant sites to accommodate strain induced by electrostatic interactions. The program is packaged with a graphical user interface and extensible to serve the needs of single-crystal diffractometer instruments that collect diffuse-scattering data.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Decoding ionic conductivity and reordering in cation-disordered pyrochlores
The ordered structure A 2 B 2 O 6 O’ in pyrochlores engenders twin rows of inequivalent anion sublattices each centred on alternating cations. While it is known that cation antisite disorder augments the ionic conductivity by several orders of magnitude, the local cation environment around the anions and the dynamic anion reordering during the cation disordering are not well-elucidated. Using atomistic simulations on Gd 2 Zr 2 O 7 , we first show that the anions engage in concerted hops to the neighbouring tetrahedral sites mostly along with the $\langle$1 0 0$\rangle$ direction while completely avoiding the octahedral sites. While the initially vacant 8 a sites start accommodating oxygen ions with increasing cation disorder, they show noticeable reluctance even at significant levels of disorder. We have also tracked both the distribution of available oxygen sites following random cation disorder, which is dependent only on cation disordering, and the probability of occupation of these sites. Interestingly, the available oxygen sites show a non-monotonic dependence on the number of B ions in the nearest neighbouring shell while the occupation probability of all the available oxygen sites increases monotonically. A tetrahedral oxygen site thus has a better probability of being occupied when it has a greater number of second neighbour B ions. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.
Science & Technology - Other Topics↗
Folded network and structural transition in molten tin
The fundamental relationships between the structure and properties of liquids are far from being well understood. For instance, the structural origins of many liquid anomalies still remain unclear, but liquid-liquid transitions (LLT) are believed to hold a key. However, experimental demonstrations of LLTs have been rather challenging. Here, we report experimental and theoretical evidence of a second-order-like LLT in molten tin, one which favors a percolating covalent bond network at high temperatures. The observed structural transition originates from the fluctuating metallic/covalent behavior of atomic bonding, and consequently a new paradigm of liquid structure emerges. The liquid structure, described in the form of a folded network, bridges two well-established structural models for disordered systems, i.e., the random packing of hard-spheres and a continuous random network, offering a large structural midground for liquids and glasses. Our findings provide an unparalleled physical picture of the atomic arrangement for a plethora of liquids, shedding light on the thermodynamic and dynamic anomalies of liquids but also entailing far-reaching implications for studying liquid polyamorphism and dynamical transitions in liquids.
36 MATERIALS SCIENCE↗
Combining enhanced sampling and deep learning dimensionality reduction for the study of the heat shock protein B8 and its pathological mutant K141E
The study provides the first 3D structural characterization of HSPB8 and its K141E mutant: extensive TREMD are combined with a deep learning algorithm to rationalize the disordered ensemble of structures adopted by each variant.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗