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At least 1,639 records · Page 91

Formation and inflammation of a turbulent jet

The formation and inflammation of a planar, turbulent jet in an incompressible medium is modeled numerically by the use of the random vortex method amended by a flame propagation algorithm. The results demonstrate the dominant influence of turbulent eddies and their interactions upon the development of the jet. Its growth is shown to consist of three stages: formation of small eddies, pairing of eddies with the same sign of circulation, and pairing of eddies of opposite signs. On this basis a number of features of the jet mechanism are revealed, namely penetration, engulfment, entrainment, and intermittency. Two cases of inflammation are considered. In one, the jet is ignited at the center of the orifice, the solution tracing its own inflammation. In the other, combustion is initiated across its full cross section, the results modeling the action of a turbulent torch as it spreads the flame into the combustible surroundings. In both cases the flow field is still dominated by the turbulent eddies and their interactions. However, the coherence among them is encumbered as a consequence of expansion due to the exothermicity of the combustion process.

Ghoniem, A. F.↗

Structural basis for microRNA targeting

MicroRNAs (miRNAs) control expression of thousands of genes in plants and animals. miRNAs function by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. In this paper, we determined crystal structures of human Argonaute-2 (Ago2) bound to a defined guide RNA with and without target RNAs representing miRNA recognition sites. These structures suggest a stepwise mechanism, in which Ago2 primarily exposes guide nucleotides (nt) 2 to 5 for initial target pairing. Pairing to nt 2 to 5 promotes conformational changes that expose nt 2 to 8 and 13 to 16 for further target recognition. Interactions with the guide-target minor groove allow Ago2 to interrogate target RNAs in a sequence-independent manner, whereas an adenosine binding-pocket opposite guide nt 1 further facilitates target recognition. Spurious slicing of miRNA targets is avoided through an inhibitory coordination of one catalytic magnesium ion. Finally, these results explain the conserved nucleotide-pairing patterns in animal miRNA target sites first observed over two decades ago.

59 BASIC BIOLOGICAL SCIENCES↗

Incubation temperature and social context affect the nest exodus of precocial ducklings

The environments that animals experience during development have important fitness consequences. In birds, parents influence the developmental environment of their offspring through incubation. Subtle changes in incubation temperature affect offspring morphology and physiology, such as growth, immune function, and thermoregulation, yet little is known about how it may affect critical early-life behaviors. Because expression of behavior can be influenced by the social environment, the effect of incubation temperature on behavior may be context-dependent. We investigated whether incubation temperature and social context influence a critical early-life task in wood ducks (Aix sponsa). Wood ducks nest in tree cavities and, shortly after hatching, ducklings must jump and climb out of the cavity. Failure to exit the nest is fatal. In 2 experiments, we incubated eggs at different mean temperatures and examined the nest exodus of ducklings individually and in mixed-incubation temperature pairs. When tested individually, ducklings incubated at 35.8 °C and 37.0 °C were ~2.5 times more successful at exiting the nest, and jumped and climbed more often, than those incubated at 35.0 °C. However, in an experiment conducted the following year, we found that social interactions mitigated these effects and there was no difference in nest exodus success when ducklings incubated at 35.0 °C and 36.0 °C were tested together in pairs. This may be because, when in pairs, ducklings incubated at the low-temperature experience social enhancement whereas those incubated at the high temperature maintain similar behaviors. Here, these results advance our understanding of how parental effects influence offspring behaviors and performance within different social contexts.

59 BASIC BIOLOGICAL SCIENCES↗

Amorphous dispersions of flubendazole in hydroxypropyl methylcellulose: Formulation stability assisted by pair distribution function analysis

Here, we use X-ray pair distribution function (PDF) analysis applied to high-energy synchrotron X-ray powder diffraction data to evaluate the amorphous solid dispersions interactions and their aging stability. The obtained systems are based on hydroxypropyl methylcellulose (hypromellose) derivatives and flubendazole (FBZ) drug dispersions prepared using a spray-dryer technique. We carry out stability studies under aging parameters (40 °C/75% relative humidity) to tune the systems’ recrystallization. The results reveal that ion-base interactions between the drug-polymer matrix are responsible for reducing clustering processes yielding slower recrystallization and different ordering in the hypromellose phthalate (HPMCP/FBZ) and hypromellose acetate succinate (HPMC-AS/FBZ) systems and complete drug clustering in hypromellose (HPMC-E3/FBZ). The structural ordering was accessed using differential X-ray PDFs that revealed the region between 3.5 Å and 5.0 Å could be related to FBZ intermolecular interactions and is more ordered for the least stable system (HPMC-E3/FBZ) and less ordered for the most stable system (HPMCP/FBZ). These results show that the ion-base interactions between drug and matrix occur at these intermolecular distances.

60 APPLIED LIFE SCIENCES↗

A surprisingly simple correlation between the classical and quantum structural networks in liquid water

Nuclear quantum effects in liquid water have profound implications for several of its macroscopic properties related to the structure, dynamics, spectroscopy, and transport. Although several of water’s macroscopic properties can be reproduced by classical descriptions of the nuclei using interaction potentials effectively parameterized for a narrow range of its phase diagram, a proper account of the nuclear quantum effects is required to ensure that the underlying molecular interactions are transferable across a wide temperature range covering different regions of that diagram. In this work, when performing an analysis of the hydrogen-bonded structural networks in liquid water resulting from the classical ( class ) and quantum ( qm ) descriptions of the nuclei with two interaction potentials that are at the two opposite ends of the range in describing quantum effects, namely the flexible, pair-wise additive q-TIP4P/F, and the flexible, polarizable TTM3-F, we found that the ( class ) and ( qm ) results can be superimposed over the temperature range T = 250-350 K using a surprisingly simple, linear scaling of the two temperatures according to T ( qm ) = α T ( class ) + Δ T , where α = 0.99 and Δ T = –6 K for q-TIP4P/F and α = 1.24 and Δ T = –64 K for TTM3-F. This simple relationship suggests that the structural networks resulting from the quantum and classical treatment of the nuclei with those two very different interaction potentials are essentially similar to each other over this extended temperature range once a model-dependent linear temperature scaling law is applied.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

Chiral Topological Superconductors Enhanced by Long-Range Interactions

We study the phase diagram and edge states of a two-dimensional p-wave superconductor with long-range hopping and pairing amplitudes. New topological phases and quasiparticles different from the usual short-range model are obtained. When both hopping and pairing terms decay with the same exponent, one of the topological chiral phases with propagating Majorana edge states gets significantly enhanced by long-range couplings. On the other hand, when the long-range pairing amplitude decays more slowly than the hopping, we discover new topological phases where propagating Majorana fermions at each edge pair nonlocally and become gapped even in the thermodynamic limit. Remarkably, these nonlocal edge states are still robust, remain separated from the bulk, and are localized at both edges at the same time. The inclusion of long-range effects is potentially applicable to recent experiments with magnetic impurities and islands in 2D superconductors.

36 MATERIALS SCIENCE↗

Particle configurations in the $NN\bar K$ system

Three-body AAB model for the $NN\bar K$(s NN = 0) kaonic cluster is considered based on the configuration space Faddeev equations. Within a single channel approach, the difference between masses of nucleons and kaons and the charge independence breaking of nucleon-nucleon interaction are taken into consideration. We definite the particle configurations in the system according to the particle masses and pair potentials. There are two sets of the particle configurations, ppK¯, npK¯ 0 and nnK¯ 0 , npK¯, charged and neutral. The three-body calculations are performed by applying NN and NK¯ phenomenological isospin-dependent potentials. The mass and energy spectra related to the particle configurations are presented. We evaluate the mass and energy uncertainties for the NNK¯ model. As a result, an analogy to NNN model for the 3 H and 3 He nuclei is proposed.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Constraints on the electron-hole pair creation energy and Fano factor below 150 eV from Compton scattering in a Skipper-CCD

Fully-depleted thick silicon Skipper-charge-coupled devices (Skipper-CCDs) have achieved sub-electron read-out noise and are an important technology to probe neutrino and light dark matter interactions. However, the successful search for rare neutrino or dark-matter events requires the signal and all backgrounds to be fully characterized. In particular, a measurement of the electron-hole pair creation energy below 150 eV and the Fano factor are necessary for characterizing the dark matter and neutrino signals. Moreover, photons from background radiation may Compton scatter in the silicon bulk, producing events that can mimic a dark matter or neutrino signal. We present a measurement of the Compton spectrum using a Skipper-CCD and a $^{241}$Am source. With these data, we measure the electron-hole pair-creation energy to be $\left(3.71 \pm 0.08\right)$ eV at 130 K in the energy range between 99.3 eV and 150 eV. By measuring the widths of the steps at 99.3 eV and 150 eV in the Compton spectrum, we introduce a novel technique to measure the Fano factor, setting an upper limit of 0.31 at 90% C.L. These results prove the potential of Skipper-CCDs to characterize the Compton spectrum and to measure precisely the Fano factor and electron-hole pair creation energy below 150 eV.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Pauling’s rules for oxide-based minerals: A re-examination based on quantum mechanical constraints and modern applications of bond-valence theory to Earth materials

Since their introduction in 1929, Pauling’s five rules have been used by scientists from many disciplines to rationalize and predict stable arrangements of atoms and coordination polyhedra in crystalline solids; amorphous materials such as silicate glasses and melts; nanomaterials, poorly crystalline solids; aqueous cation and anion complexes; and sorption complexes at mineral-aqueous solution interfaces. The predictive power of these simple yet powerful rules was challenged recently by George et al. (2020), who performed a statistical analysis of the performance of Pauling’s five rules for about 5000 oxide crystal structures. They concluded that only 13% of the oxides satisfy the last four rules simultaneously and that the second rule has the most exceptions. They also found that Pauling’s first rule is satisfied for only 66% of the coordination environments tested and concluded that no simple rule linking ionic radius to coordination environment will be predictive due to the variable quality of univalent radii. We address these concerns and discuss quantum mechanical calculations that complement Pauling’s rules, particularly his first (radius sum and radius ratio rule) and second (electrostatic valence rule) rules. We also present a more realistic view of the bonded radii of atoms, derived by determining the local minimum in the electron density distribution measured along trajectories between bonded atoms known as bond paths, i.e., the bond critical point (rc). Electron density at the bond critical point is a quantum mechanical observable that correlates well with Pauling bond strength. Moreover, a metal atom in a polyhedron has as many bonded radii as it has bonded interactions, resulting in metal and O atoms that may not be spherical. O atoms, for example, are not spherical in many oxide-based crystal structures. Instead, the electron density of a bonded oxygen is often highly distorted or polarized, with its bonded radius decreasing systematically from ~1.38 Å when bonded to highly electropositive atoms like sodium to 0.64 Å when bonded to highly electronegative atoms like nitrogen. Bonded radii determined for metal atoms match the Shannon (1976) radii for more electropositive atoms, but the match decreases systematically as the electronegativities of the M atoms increase. As a result, significant departures from the radius ratio rule in the analysis by George et al. (2020) is not surprising. We offer a modified, more fundamental version of Pauling’s first rule and demonstrate that the second rule has a one-to-one connection between the electron density accumulated between the bonded atoms at the bond critical point and the Pauling bond strength of the bonded interaction. Pauling’s second rule implicitly assumes that bond strength is invariant with bond length for a given pair of bonded atoms. Many studies have since shown that this is not the case, and Brown and Shannon (1973) developed an equation and a set of parameters to describe the relation between bond length and bond strength, now redefined as bond valence to avoid confusion with Pauling bond-strength. Brown (1980) used the valence-sum rule, together with the path rule and the valence-matching principle, as the three axioms of bond-valence theory (BVT), a powerful method for understanding many otherwise elusive aspects of crystals and also their participation in dynamic processes. We show how a priori bond-valence calculations can predict unstrained bond-lengths and how bond-valence mapping can locate low-Z atoms in a crystal structure (e.g., Li) or examine possible diffusion pathways for atoms through crystal structures. In addition, we briefly discuss Pauling’s third, fourth, and fifth rules, the first two of which concern the sharing of polyhedron elements (edges and faces) and the common instability associated with structures in which a polyhedron shares an edge or face with another polyhedron and contains high-valence cations. The olivine [α-(MgxFe1–x)2SiO4] crystal structure is used to illustrate the distortions from hexagonal close-packing of O atoms caused by metal-metal repulsion across shared polyhedron edges. We conclude by discussing several applications of BVT to Earth materials, including the use of BVT to: (1) locate H+ ions in crystal structures, including the location of protons in the crystal structures of nominally anhydrous minerals in Earth’s mantle; (2) determine how strongly bonded (usually anionic) structural units interact with weakly bonded (usually cationic) interstitial complexes in complex uranyl-oxide and uranyl-oxysalt minerals using the valence-matching principle; (3) calculate Lewis acid strengths of cations and Lewis base strengths of anions; (4) determine how (H2O) groups can function as bond-valence transformers by dividing one bond into two bonds of half the bond valence; (5) help characterize products of sorption reactions of aqueous cations (e.g., Co2+ and Pb2+) and oxyanions [e.g., selenate (Se6+O4)2- and selenite (Se4+O3)2-] at mineral-aqueous solution interfaces and the important role of protons in these reactions; and (6) help characterize the local coordination environments of highly charged cations (e.g., Zr4+, Ti4+, U4+, U5+, and U6+) in silicate glasses and melts.

Geochemistry & Geophysics↗

pH‐ and Redox‐Responsive Pickering Emulsions Based on Cellulose Nanocrystal Surfactants

Abstract Nanoparticle surfactants (NPSs), formed by using dynamic interactions between nanoparticles and complementary ligands at the liquid‐liquid interface, have emerged as “smart emulsifiers” with attributes of high emulsification efficiency, long‐term stability, and on‐demand emulsification/demulsification capabilities. However, only pH‐responsiveness can be adopted for the assembly of reported NPSs formed by electrostatic interactions. Here, we propose an alternative design strategy, by taking advantage of the ferrocenium (Fc + ) sulfate ion pair, to develop a new type of cellulose nanocrystal (CNC) surfactant. The Fc + groups are sensitive to pH, redox reagents and voltage, imparting the CNC surfactants and derived Pickering emulsions with multi‐stimuli‐responsiveness, and showing promising applications in controllable delivery, release, and biphasic biocatalysis.

Yang, Yang↗

pH- and Redox-Responsive Pickering Emulsions Based on Cellulose Nanocrystal Surfactants

Nanoparticle surfactants (NPSs), formed by using dynamic interactions between nanoparticles and complementary ligands at the liquid-liquid interface, have emerged as “smart emulsifiers” with attributes of high emulsification efficiency, long-term stability, and on-demand emulsification/demulsification capabilities. However, only pH-responsiveness can be adopted for the assembly of reported NPSs formed by electrostatic interactions. Here, we propose an alternative design strategy, by taking advantage of the ferrocenium (Fc + ) sulfate ion pair, to develop a new type of cellulose nanocrystal (CNC) surfactant. In conclusion, the Fc + groups are sensitive to pH, redox reagents and voltage, imparting the CNC surfactants and derived Pickering emulsions with multi-stimuli-responsiveness, and showing promising applications in controllable delivery, release, and biphasic biocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adsorptive removal of Sb(V) from water using a mesoporous Zr-based metal–organic framework

Here, the adsorption and removal of Sb(OH) 6 - from water using the water stable Zr 6 -based MOF, NU-1000, is explored. The adsorption capacity and uptake time of Sb(OH) 6 - in NU-1000 is measured at varying concentrations to determine an overall maximum adsorption capacity of 260 mg of Sb(OH) 6 - per g of MOF, corresponding to 2.5 Sb(OH) 6 - per node of NU-1000 and exhibiting the highest adsorption capacity of any material reported to date for Sb(V) removal. Differential pair distribution function (dPDF) analysis of total X-ray scattering data reveals that Sb(OH) 6 - interacts in an η 2 μ 2 fashion with the Zr 6 -node of NU-1000, and that as the amount of Sb(OH) 6 - adsorbed increases, the interaction between the analyte and the node becomes stronger. Post-adsorption characterization shows that NU-1000 remains stable throughout the adsorption process.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Ultrafast Correlation Energy Estimator

A virtually no-cost method is proposed that can compute the correlation energies of general, covalently bonded, organic, and inorganic molecules (including conjugated π-electron systems) with a well-defined dominant Lewis structure at the accuracy of 99.5% of the near-exact values determined by the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] in the complete-basis-set (CBS) limit. This Correlation Energy Per Bond (CEPB) method assigns a partial correlation energy to each bond type (characterized by the identities of the two atoms forming the bond and its integer bond order) and to a lone pair, regardless of the bond length, bond angle, sp-hybridization, π-electron conjugation, ionicity, noncovalent interactions, etc. At its current stage, the method is mainly suitable for near-equilibrium geometries. The correlation energies per bond are determined by a fit to the CCSD(T)/CBS benchmarks. It can neither improve the equilibrium structures nor discern conformers or positional isomers, yet its accuracy for reaction energies rivals that of the second-order Møller–Plesset perturbation theory, which is far more expensive. Its promising performance underscores the possibility that surprisingly compact, chemically intuitive molecular fragments exist into which correlation energies can be partitioned, leading to various ultrafast correlation-energy estimators tailored to different purposes.

Binding energy↗

Surface Atomic Structure and Functionality of Metallic Nanoparticles: A Case Study of Au–Pd Nanoalloy Catalysts

The surface atomic structure of metallic nanoparticles (NPs) plays a key role in shaping their physicochemical properties and response to external stimuli. Not surprisingly, current research increasingly focuses on exploiting its prime characteristics, including the amount, location, coordination, and electronic configuration of distinct surface atomic species, as tunable parameters for improving the functionality of metallic NPs in practical applications. The effort requires clear understanding of the extent to which changes in each of these characteristics would contribute to achieving the targeted functionality. This, in the first place, requires good knowledge of the actual surface of metallic NPs at atomic level. Through a case study on Au–Pd nanoalloy catalysts of industrial and environmental importance, we demonstrate that the surface atomic structure of metallic NPs can be determined in good detail by resonant high-energy X-ray diffraction (HE-XRD). Furthermore, using our experimental surface structure and CO oxidation activity data, we shed new light on the elusive origin of the remarkable catalytic synergy between surface Au and Pd atoms in the nanoalloys. In particular, we show that it arises from the formation of a specific “skin” on top of the nanoalloys that involves as many unlike, i.e., Au–Pd and Pd–Au, atomic pairs as possible given the overall chemical composition of the NPs. Moreover, unlike atoms from the “skin” interact strongly, including both changing their size and electronic structure in inverse proportions. That is, Au atoms shrink and acquire a partial positive charge of 5d-character whereas Pd atoms expand and become somewhat 4d-electron deficient. Accordingly, the reactivity of Au increases whereas Pd atoms become less reactive, as compared to atoms at the surface of pure Au and Pd NPs, respectively. Ultimately, this renders Au–Pd alloy NPs superb catalysts for CO oxidation reaction over a broad range of alloy compositions. Our findings are corroborated by DFT calculations based on a refined version of d-band center theory on the catalytic properties of late transition metals and alloys. Here, we discuss opportunities for improving the accuracy of current theory on surface-controlled properties of metallic NPs through augmenting the theory with surface structure data obtained by resonant XRD.

36 MATERIALS SCIENCE↗

The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site

The Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM) methylates the adenine of hemimethylated GANTC after replication. Here we present the structure of CcrM in complex with double-stranded DNA containing the recognition sequence. CcrM contains an N-terminal methyltransferase domain and a C-terminal nonspecific DNA-binding domain. CcrM is a dimer, with each monomer contacting primarily one DNA strand: the methyltransferase domain of one molecule binds the target strand, recognizes the target sequence, and catalyzes methyl transfer, while the C-terminal domain of the second molecule binds the non-target strand. The DNA contacts at the 5-base pair recognition site results in dramatic DNA distortions including bending, unwinding and base flipping. The two DNA strands are pulled apart, creating a bubble comprising four recognized base pairs. The five bases of the target strand are recognized meticulously by stacking contacts, van der Waals interactions and specific Watson–Crick polar hydrogen bonds to ensure high enzymatic specificity.

59 BASIC BIOLOGICAL SCIENCES↗