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137 records · Page 8

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof of principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. In conclusion, our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.

HIV-1 dimerization initiation site↗

A convergence metric for counting statistics in time-resolved small angle neutron scattering

Here, this work introduces a model-independent, dimensionless metric for predicting optimal measurement duration in time-resolved small-angle neutron scattering using early-time data. Built on a Gaussian process regression framework, the method reconstructs scattering profiles with quantified uncertainty, even from sparse or noisy measurements. Demonstrated on the EQ-SANS instrument at the Spallation Neutron Source, the approach generalizes to general SANS instruments with a two-dimensional detector. A key result is the discovery of a dimensionless convergence metric revealing a universal power-law scaling in profile evolution across soft matter systems. When time is normalized by a system-specific characteristic time t*, the variation in inferred profiles collapses onto a single curve with an exponent between −2 and −1. This trend emerges within the first ten time steps, enabling early prediction of measurement sufficiency. The method supports real-time experimental optimization and is especially valuable for maximizing efficiency in low-flux environments such as compact accelerator-based neutron sources.

Tung, Chi-Huan [Oak Ridge National Laboratory (ORN↗

Porosity in nuclear graphite and its impact on nuclear reactor science and criticality safety applications

Porosity in nuclear-grade graphite significantly influences its low-energy neutron scattering, yet its effect on underlying phonon properties remains debated. Here, this work integrates inelastic and small-angle neutron scattering (INS/SANS) experiments, advanced atomistic simulations with a novel machine-learned potential (DeepMD), total cross-section measurements, and neutronics calculations (SCALE, MCNP, OpenMC) to investigate porosity’s impact on neutron thermalization. INS measurements on diverse graphite grades reveal no discernible porosity effect on phonon spectra, which align with crystalline graphite. Conversely, total cross-section data below ≈10 meV show increased scattering attributable to SANS. Our DeepMD simulations demonstrate that realistic micropores do not distort phonon spectra, challenging the assumptions in current ENDF/B-VIII.1 porosity thermal scattering laws (TSLs). These TSLs, based on random atom removal, produce unphysical phonon spectra and inflate inelastic cross-sections. Augmenting a crystalline TSL with an SANS component accurately captures experimental total cross-sections. Neutronics benchmarks (ICSBEP/IRPhE) show ENDF porosity TSLs unphysically increase neutron multiplication factor, keff. Crucially, incorporating SANS physics (NCrystal/OpenMC) indicates accurately modeled porosity negligibly affects keff, reactor physics, or criticality safety.

Critical benchmarks↗

Emergent Nanostructure and Ion Transport in Polyzwitterion/Polyanion Blends

Solid polymer electrolytes (SPEs) hold great promise for the advancement of next-generation energy storage devices. However, the ion transport mechanism in SPEs remains poorly understood. In this study, we investigate blends of poly(1-(3-sulfonatopropyl)-2-vinylpyridinium) (P2VPPS) and poly(lithium (trifluoromethane)sulfonimide methacrylate) (P(MTFSI)Li) of varying molar ratios to develop a mechanistic understanding of ionic conductivity in a miscible polyzwitterion/polyanion system. Polyanions can act as single-ion conductors, but conductivity is often prohibitively low due to the decreased segmental mobility and ion aggregation. Here, it is hypothesized that the introduction of a polyzwitterion would competitively interact with the polyanion charge groups to realize improvements in the conductivity. Attractive interactions between the polyanions and polyzwitterions are confirmed by the blend’s increased glass transition temperature using the Gordon–Taylor equation. Notably, an ordered local nanostructure (∼24 Å) emerged in the P2VPPS/P(MTFSI)Li system at certain compositions, as characterized by small-angle X-ray and neutron scattering (SAXS/SANS). Concurrent with the emergence of this structure, broadband dielectric spectroscopy confirmed improvements in ionic conductivity. The highest conductivity is observed at a specific blend ratio P2VPPS:P(MTFSI)Li = 0.2:1 in the glassy state and 0.3:1 in the rubbery state, corresponding to the lowest effective activation energy (E*). Coarse-grained molecular dynamics simulations further emphasize the role of complexation between polyzwitterion and polyanion chains, correlating with the emergence of a new peak in SAXS and SANS for the blends. This work provides a fresh perspective on the role of local structural design in developing SPEs and offers insights into the morphological effects on ionic conductivity.

chemical structure↗

Preferred Void Orientation in Uniaxially Pressed PBX 9502

Ultra- and small-angle neutron scattering techniques were used to study the morphology of voids in directions parallel and perpendicular to the compaction plane of a uniaxially pressed cylinder of PBX 9502. Two-dimensional scattering patterns from samples cut parallel to the compaction plane had circular equal-intensity contours, implying that along this view the voids are circular or randomly oriented. Identical measurements of samples cut perpendicular to the compaction plane produced elliptical equal-intensity contours, indicating preferred orientation of voids. Analysis of the two dimensional scattering patterns confirmed that the voids are non-spherical with an average aspect ratio of 1.20, flattened so that the larger dimensions of the voids lie within the compaction plane. Model analysis of the combined ultra- and small-angle neutron scattering curves revealed that the PBX 9502 porosity is interconnected, in the form of aggregates comprised of non-spherical, primary voids. The volume dimension was found to be the same in both directions, indicating that the aggregate is randomly oriented throughout the sample, and that it is the primary voids that are preferentially oriented. Furthermore, void interfaces with the surrounding matrix were found to be rough or polydisperse, with a common roughness dimension or polydispersity in all directions.

42 ENGINEERING↗

Optimization of neutron chopper and optics for CENTAUR, the SANS/WANS diffractometer at the spallation neutron source second target station

Herein this report presents the physics design and optimization of the neutron chopper and optics systems for the CENTAUR instrument, a multifunctional small-angle and wide-angle neutron scattering diffractometer for the Spallation Neutron Source Second Target Station. This instrument will offer a wide range of capabilities, including small-angle neutron scattering with wide Q coverage (e.g., 0.001–20 Å –1 ), providing a tool to investigate structures from atomic to mesoscopic scales simultaneously. To efficiently transport desired neutrons from the compact high-brightness cold source, several innovative designs are utilized: a time-zero chopper with a straight guide system for short-wavelength neutrons, octagonal guides for higher flux, and a correlation chopper to reduce inelastic scattering. The optimization process considers factors such as useable time-integrated flux, instrument resolution, brilliance transfer, divergence, and acceptance diagram uniformity. The overall design prioritizes flexibility to accommodate diverse user requirements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Influence of microstructure on replacement and porosity generation during experimental dolomitization of limestones

Replacement reactions commonly alter the multiscale pore structures of rocks during fluid-rock interactions. Analysis of these processes in various model fluid-rock systems during controlled laboratory experiments provides insights into the origins of microstructures found in natural materials. This study focused on understanding the effects of initial starting material permeability and resultant differences in transport pathways on porosity and mineralogical changes during limestone dolomitization.A series of replacement experiments (32–317 days in duration) have been conducted in which 1.59 cm (5/8 in.) diameter cores of two different limestones were reacted with saturated MgCl2 solutions at 200 °C. The Texas Cream (Austin Chalk) is a high-porosity, high-permeability limestone, whereas both the porosity and permeability of the Carthage Marble (Burlington Limestone) are relatively low. Altered limestones were imaged using scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF–SIMS) and electron microprobe analysis (EMPA). A representative grain boundary of the low-porosity limestone was targeted for a focused ion beam (FIB) lift-out and characterized using transmission electron microscopy (TEM). These results were coupled with analyses of radial changes in the porosity distribution of the core derived from X-ray and neutron small- and ultra-small angle scattering ((U)SANS/(U)SAXS).The high-porosity/permeability limestone showed a four times faster bulk replacement rate than the lower-porosity/permeability material, and a different mechanism of porosity development. For the low-porosity limestone, a two-stage replacement occurred, with the reacted region of the core consisting of an inner rim in which the limestone was replaced by two calcite-dolomite solid solutions, and an outer rim in which the dolomite was replaced by magnesite. Elongated pores formed along grain boundaries at the initial limestone/dolomite reaction interface, and additional nanometer-scale porosity was formed at the secondary magnesite replacement rim. Grain boundaries were identified as preferential pathways for transport leading to dolomitization and a grain boundary diffusion rate was calculated based on microstructural characterization. In contrast, replacement in the high-porosity limestone was accompanied by porosity generation through replacement of individual grains by dolomite throughout the sample and, in longer runs, magnesite in outer parts of the core. These observations emphasize that both the mechanisms of the replacement reaction and the microstructure and chemistry of the replaced product are contingent on the initial structure of the starting material.

36 MATERIALS SCIENCE↗

Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF)

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis , using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (Δ fadN ) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA- fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n 16:0 to a 15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

59 BASIC BIOLOGICAL SCIENCES↗

Rheology and dynamics of a solvent segregation driven gel (SeedGel)

Bicontinuous structures promise applications in a broad range of research fields, such as energy storage, membrane science, and biomaterials. Kinetically arrested spinodal decomposition is found responsible for stabilizing such structures in different types of materials. A recently developed solvent segregation driven gel (SeedGel) is demonstrated to realize bicontinuous channels thermoreversibly with tunable domain sizes by trapping nanoparticles in a particle domain. As the mechanical properties of SeedGel are very important for its future applications, a model system is characterized by temperature-dependent rheology. The storage modulus shows excellent thermo-reproducibility and interesting temperature dependence with the maximum storage modulus observed at an intermediate temperature range (around 28 °C). SANS measurements are conducted at different temperatures to identify the macroscopic solvent phase separation during the gelation transition, and solvent exchange between solvent and particle domains that is responsible for this behavior. Further, the long-time dynamics of the gel is further studied by X-ray Photon Correlation Spectroscopy (XPCS). The results indicate that particles in the particle domain are in a glassy state and their long-time dynamics are strongly correlated with the temperature dependence of the storage modulus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data Reproducibility of Spin-Echo Small-Angle Neutron Scattering Instruments

Spin-echo small-angle neutron scattering (SESANS) is a unique method to measure structures of materials in real space with length scales from ∼ 30 μm to ∼20 µm. As shown in Figure 1, the accessible length scale of SESANS is given by its ability to encode the momentum transfer into the Larmor phase, namely Φ = $\vec{𝛿}$ ⋅ $\vec{𝑄}$, where $\vec{𝑄}$ is the momentum transfer and $\vec{𝛿}$ is the encoding vector of the setup and its projection along Q (δQ) is called spin-echo length (SEL). The spin echo length, which is synonymous with the spatial correlation distance probed, is defined as the following 𝛿𝑄 ∝ 𝜆 2 𝐵𝐿cot𝜃 where 𝜆 is neutron wavelength, B is magnetic field, L is length of the parallelogram magnetic field region, and 𝜃 is the angle between the inclined magnetic field boundary and the beam direction, as shown in Figure 1. The result of the SESANS experiment is a Hankel transformation of the SANS scattering function I(Q), which yields the correlation function of the sample in real space.

47 OTHER INSTRUMENTATION↗