Structural insight into the novel iron-coordination and domain interactions of transferrin-1 from a
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Weber, Jacob J.↗
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Chemical interactions that govern the structures of metals
Most metals adopt simple structures such as body-centered cubic (BCC), face-centered cubic (FCC), and hexagonal close-packed (HCP) structures in specific groupings across the periodic table, and many undergo transitions to surprisingly complex structures on compression, not expected from conventional free-electron-based theories of metals. First-principles calculations have been able to reproduce many observed structures and transitions, but a unified, predictive theory that underlies this behavior is not yet in hand. Discovered by analyzing the electronic properties of metals in various lattices over a broad range of sizes and geometries, a remarkably simple theory shows that the stability of metal structures is governed by electrons occupying local interstitial orbitals and their strong chemical interactions. The theory provides a basis for understanding and predicting structures in solid compounds and alloys over a broad range of conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Swine Host Protein Coiled-Coil Domain-Containing 115 (CCDC115) Interacts with Classical Swine Fever Virus Structural Glycoprotein E2 during Virus Replication
Interactions between the major structural glycoprotein E2 of classical swine fever virus (CSFV) with host proteins have been identified as important factors affecting virus replication and virulence. Previously, using the yeast two-hybrid system, we identified swine host proteins specifically interacting with CSFV E2. In this report, we use a proximity ligation assay to demonstrate that swine host protein CCDC115 interacts with E2 in CSFV-infected swine cells. Using a randomly mutated E2 library in the context of a yeast two-hybrid methodology, specific amino acid mutations in the CSFV E2 protein responsible for disrupting the interaction with CCDC115 were identified. A recombinant CSFV mutant (E2ΔCCDC115v) harboring amino acid changes disrupting the E2 protein interaction with CCDC115 was produced and used as a tool to assess the role of the E2–CCDC115 interaction in viral replication and virulence in swine. CSFV E2ΔCCDC115v showed a slightly decreased ability to replicate in the SK6 swine cell line and a greater replication defect in primary swine macrophage cultures. A decreased E2–CCDC115 interaction detected by PLA is observed in cells infected with E2ΔCCDC115v. Importantly, animals intranasally infected with 105 TCID50 of E2ΔCCDC115v experienced a significantly longer survival period when compared with those infected with the parental Brescia strain. This result would indicate that the ability of CSFV E2 to bind host CCDC115 protein during infection plays an important role in virus replication in swine macrophages and in virus virulence during the infection in domestic swine.
59 BASIC BIOLOGICAL SCIENCES↗
Dephasing of ion beams as magnetic vortex acceleration regime transitions into a bubble-like field structure
The interaction of an ultra-intense laser pulse with a near critical density target results in the formation of a plasma channel, a strong azimuthal magnetic field and moving vortices. An application of this is the generation of energetic and collimated ion beams via magnetic vortex acceleration. The optimized regime of magnetic vortex acceleration is becoming experimentally accessible with new high intensity laser beamlines coming online and advances made in near critical density target fabrication. The robustness of the acceleration mechanism with realistic experimental conditions is examined with three-dimensional simulations. Of particular interest is the acceleration performance with different laser temporal contrast conditions, in some cases leading to pre-expanded target profiles prior to the arrival of the main pulse. Preplasma effects on the structure of the accelerating fields are explored, including a detailed analysis of the ion beam properties and the efficiency of the process. Improved scaling laws for the magnetic vortex acceleration mechanism, including the laser focal spot size effects, are presented.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Magnetohydrodynamic Wave Mode Conversion in a Pseudostreamer Structure
The interaction of a fast magnetoacoustic wave with a magnetic null point in a pseudostreamer magnetic configuration is modeled. The incident fast wave is excited by an impulsive velocity driver located in the corona outside the Alfvén-acoustic equipartition layer. The fast wave front experiences refraction and wraps around the null point, while the front segment approaching the null point along the magnetic bisector passes through it. In the equipartition layer surrounding the null point, part of the fast wave energy is converted into slow magnetoacoustic waves. Slow waves propagate outward from the null point along the magnetic separatrices. The fronts of slow waves exhibit a characteristic chevron shape. The fast-to-slow mode conversion efficiency increases with the width of the initial perturbation, following a power-law dependence with an index of approximately 1.06. For initial wave amplitudes below about 10% of the local Alfvén speed, the dependence of the conversion efficiency on the initial amplitude is weak. After interacting with the null point, the amplitudes of the fast waves decrease significantly owing to energy conversion and the spreading of wave energy over a broad spatial domain. In contrast, the energy of slow waves remains concentrated in the vicinity of the magnetic separatrices, resulting in less pronounced geometric attenuation of these waves. These findings are consistent with observational reports of the interaction of a coronal fast wave with a pseudostreamer.
Zhong, Yu [Univ. of Warwick, Coventry (United King↗
Li 4 Ru 2 OCl 10 ·10H 2 O: crystal structure, magnetic properties and bonding interactions in ruthenium-oxo complexes
The results of the structural determination, magnetic characterization, and theoretical calculations of a new ruthenium-oxo complex, Li 4 [Ru 2 OCl 10 ]·10H 2 O, are presented. Single crystals were grown using solvent methods and the crystal structure was characterized by single crystal X-ray diffraction. Li 4 [Ru 2 OCl 10 ]·10H 2 O crystallizes into a low-symmetry triclinic structure ($P\bar1$) due to the much smaller Li + cation compared to K + cation in the tetragonal complex K 4 [Ru 2 OCl 10 ]·H 2 O. The X-ray photoelectron spectra confirm only the single valent Ru 4+ in Li 4 [Ru 2 OCl 10 ]·10H 2 O even though two distinct Ru sites exist in the crystal structure. Magnetic measurements reveal the diamagnetic property of Li 4 [Ru 2 OCl 10 ]·10H 2 O with unpaired electrons existing on Ru 4+ . Furthermore, the molecular orbital analysis matches well with the observed UV and magnetic measurements.
36 MATERIALS SCIENCE↗
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities
Abstract The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.
Biotechnology & Applied Microbiology↗
High throughput, accurate gene annotation through AI and HPC-enabled structural analysis
With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.
59 BASIC BIOLOGICAL SCIENCES↗
High resolution crystal structure of NaTrxh from Nicotiana alata and its interaction with the S-RNase
Not Available
Torres-Rodríguez, María Daniela↗
Supersymmetric Massive Gravity
We initiate a systematic study of the self-interactions of a massive spin-2 “graviton” consistent with up to N = 4 supersymmetry. Using a recently developed massive on-shell superspace formalism, we construct the most general set of cubic massive graviton amplitudes in a form with all supersymmetry and Lorentz invariance manifest. We find that for N ≥ 3 supersymmetry, the family of consistent interactions coincide with those of the ghost-free dRGT model. For N = 4 (maximal) supersymmetry there is a single consistent cubic interaction which coincides with the unique structure required for the absence of asymptotic superluminality. Additionally, we discuss the structure of interactions in the high-energy limit, connections to supersymmetric Galileons and the possibility of a supersymmetric massive double copy.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
A UHM–ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Compositing and Characterization of SE Quadrant Waste Exemplars
This report outlines the experimental investigation and characterization of transport properties in Hanford SE quadrant High-Level Waste (HLW). The goal of the study was to establish baseline behaviors of bulk composite rheology and settling characteristics to facilitate waste treatment process design for the Waste Treatment and Immobilization Plant (WTP) and avoid waste conditions and properties favorable to bubble cascade gas release events. The study focused on two major objectives: 1) identifying, obtaining, and preparing relevant Hanford tank waste samples for evaluation and 2) quantifying the “as-received” rheology and transport properties of the samples. Twenty-three centrifuged core segments originating from tanks AN-101, AN-106, and AW-105 were selected based on compositional relevance to SE quadrant PUREX cladding waste. These materials were composited into five waste composites enriched with target analytes: aluminum (Al), iron (Fe), phosphate (PO 4 ), uranium (U), and zirconium (Zr). Physical property and transport testing examined particle size distributions, bulk densities, settling behaviors, rheological properties, shear strengths, and just-suspended mixing speeds (NJS). Testing revealed two distinct composite classifications based on rheological characteristics: non-Newtonian composites (Fe and PO 4 ) and Newtonian composites (Al, U, and Zr). The Fe and PO 4 composites exhibited slow settling rates and reduced mobilization proclivity, attributable to strong particle-particle interactions and the formation of yield structures within non-Newtonian slurries. In contrast, the Al, U, and Zr composites displayed rapid settling and dense compaction behaviors, indicative of minimal structuring and interactions. Shear strengths for all composites were generally low relative to prior studies of SE quadrant waste, with only the U composite showing elevated strength approaching values reported in previous literature. Repeat shear strength measurements revealed contributions from dense granular material in the U composite and stronger cohesive properties in the Al composite. Settling data highlighted hindered settling behavior, with rates falling more than one order of magnitude below estimates based on Stokes’ law and rate decreasing as composite UDS content increased. NJS testing demonstrated different mobilization behaviors between cohesive and granular composites. The Fe composite required the highest mixing rate for resuspension, while the Al composite was the easiest to resuspend. Comparison of measured NJS against predictions made using the Zwietering correlation suggests non-Newtonian behavior alters resuspension mechanics, rendering non-Newtonian systems more stable against resuspension lift forces relative to their granular counterparts.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Soil microenvironmental variation drives below‐ground trait variation and interacts with macroclimate to structure above‐ground trait variation of arctic shrubs
Abstract Intraspecific trait variation can influence plant performance in different environments and may thereby determine the ability of individual plants to respond to climate change. However, our understanding of its patterns and environmental drivers across different spatial scales is incomplete, especially in understudied regions like the Arctic. To fill this knowledge gap, we examined above‐ground and below‐ground traits from three shrub taxa expanding across the tundra biome and evaluated their relationships with multiple microenvironmental and macroclimatic factors. The traits reflected plant size and structure (plant height, leaf area and root to shoot ratio), leaf economics (specific leaf area, nitrogen content), and root economics and collaboration with mycorrhizal fungi (specific root length, root tissue density, nitrogen content, and ectomycorrhizal colonisation intensity). We also measured leaf and root δ 15 N and leaf δ 13 C to characterise nitrogen source and acquisition pathways and plant water stress. Traits were measured in replicated plots ( N = 135) varying in soil microclimate, thaw depth and organic layer thickness established across five sites spanning a macroclimate gradient in northern Alaska. This hierarchical design allowed us to disentangle the independent and combined effects of fine‐scale and broad‐scale factors on intraspecific trait variation. We found substantial intraspecific variation at fine spatial scales for most traits and less variation along the macroclimate gradient and between shrub taxa. Consistent with these patterns, microenvironmental factors, mainly soil moisture and thaw depth, interacted with macroclimate, mainly climatic water deficit, to structure size‐structural and leaf trait variation. In contrast, most root traits responded additively to thaw depth and macroclimate. Synthesis . Our results demonstrate that above‐ground and below‐ground tundra shrub traits respond differently to microenvironmental and macroclimatic variation. These differing responses contribute to substantial trait variation at fine spatial scales and may decouple above‐ground and below‐ground trait responses to climate change.
Environmental Sciences & Ecology↗
Ionic Liquids in Analytical Chemistry: Fundamentals, Technological Advances, and Future Outlook
The development of new analytical methods most often focus on novel materials used to impart selectivity or sensitivity to the protocol. Ionic liquids (ILs) are a class of solvents that have been extensively explored as promising materials for various applications and continue to be explored due to their tunable physicochemical properties. These materials possess melting temperatures below 100 °C and can interact with analytes through a multitude of interactions afforded by their readily tunable chemical structure. These interactions include electrostatic, dispersive, hydrogen bonding, π–π, and dipolar interactions and can be modulated or strengthened based on the functional groups present within the chemical structure. ILs consist predominately of organic cations and either inorganic or organic anions, both of which can be functionalized with desired moieties. Common cation and anions found in IL chemical structures are presented in Figure 1. The unique polarity afforded by the ionic structure has also led to their increasing use in areas including sample preparation, chemical separations, electrochemistry, mass spectrometry, and spectroscopy.
Zeger, Victoria R. [Iowa State Univ., Ames, IA (Un↗
Closing the Gap Between Modeling and Experiments in the Self-assembly of Biomolecules at Interfaces and in Solution
Molecular self-assembly is a powerful tool in materials design, wherein non-covalent interactions like electrostatic, hydrophobic, hydrogen bonding, and van der Waals can be exploited to produce supramolecular nanostructures that are functional and highly tunable. Biomolecules are attractive building blocks, as they are biocompatible, biodegradable and adopt a wide array of higher order structures. Moreover, naturally occurring protein systems display a manifold of structures and interactions that can be replicated in synthetic biomolecules. In this perspective, we highlight advances in multiscale simulation techniques across broad spatiotemporal scales that can aid in characterizing self-assembly of hybrid and hierarchical bionanomaterial systems, with an emphasis on physics-based simulation approaches currently employed to study biomolecules at mineral interfaces. The power of these approaches is highlighted across a few recent areas where molecular simulations have advanced our understanding of self-assembly spanning peptides to protein self-assembly. Looking forward, we discuss how in the near future emerging methods in statistical and machine learning will advance this research field in all areas from expanding the capabilities of physics-based simulation methods to enabling new analyses of high throughput experiments. These advances will pave the way for understanding the molecular recognition patterns in systems that are dictated by self-assembly - biomineralizing peptides, hierarchical peptoids, and large protein assemblies, and will aid in the development of a new synthesis science for achieving precise molecular control in materials design
Sampath, Janani↗
Interaction of HOMs in periodic accelerating structures
The paper discusses the HOM interaction effect in a 5-cell 650 MHz HB cavity prototype for the PIP-II project. This effect may lead to flat HOM passbands. In the presence of misalignments, this passband disintegrates into individual cell resonances that are not coupled to the beam pipes and, therefore, have a high-quality factor and R/Q ratio. These resonances can lead to excessive cryogenic loading, increased emittance, and beam instabilities. An analytical theory has been developed to explain this effect, as well as special methods for eliminating it.
Yakovlev, V. [Fermilab]↗
Measurements of $t\overline tH$ Production and the CP Structure of the Yukawa Interaction between the Higgs Boson and Top Quark in the Diphoton Decay Channel
The first observation of the t t ¯ H process in a single Higgs boson decay channel with the full reconstruction of the final state ( H → γ γ ) is presented, with a significance of 6.6 standard deviations ( σ ). The C P structure of Higgs boson couplings to fermions is measured, resulting in an exclusion of the pure C P -odd structure of the top Yukawa coupling at 3.2 σ . The measurements are based on a sample of proton-proton collisions at a center-of-mass energy s = 13 TeV collected by the CMS detector at the LHC, corresponding to an integrated luminosity of 137 fb – 1 . The cross section times branching fraction of the t t ¯ H process is measured to be σ t t ¯ H B γ γ = 1.56 – 0.32 + 0.34 fb , which is compatible with the standard model prediction of 1.13 – 0.11 + 0.08 fb . The fractional contribution of the C P -odd component is measured to be f C P H t t = 0.00 ± 0.33 .
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Effect of water on eutectic solvents: Structural properties and physical interactions with CO2
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗