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At least 1,225 records · Page 68

Structural and biochemical insights into NEIL2’s preference for abasic sites

Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

1000 Wh L−1 lithium-ion batteries enabled by crosslink-shrunk tough carbon encapsulated silicon microparticle anodes

Abstract Microparticulate silicon (Si), normally shelled with carbons, features higher tap density and less interfacial side reactions compared to its nanosized counterpart, showing great potential to be applied as high-energy lithium-ion battery anodes. However, localized high stress generated during fabrication and particularly, under operating, could induce cracking of carbon shells and release pulverized nanoparticles, significantly deteriorating its electrochemical performance. Here we design a strong yet ductile carbon cage from an easily processing capillary shrinkage of graphene hydrogel followed by precise tailoring of inner voids. Such a structure, analog to the stable structure of plant cells, presents ‘imperfection-tolerance’ to volume variation of irregular Si microparticles, maintaining the electrode integrity over 1000 cycles with Coulombic efficiency over 99.5%. This design enables the use of a dense and thick (3 mAh cm–2) microparticulate Si anode with an ultra-high volumetric energy density of 1048 Wh L–1 achieved at pouch full-cell level coupled with a LiNi0.8Co0.1Mn0.1O2 cathode.

25 ENERGY STORAGE↗

A 16 deg2 survey of emission-line galaxies at z < 1.6 from HSC-SSP PDR2 and CHORUS

Abstract We have conducted a comprehensive survey of emission-line galaxies at z ≲ 1.6 based on narrow-band (NB) imaging data taken with Hyper Suprime-Cam (HSC) on the Subaru telescope. In this paper, we update the catalogs of Hα, [O iii], and [O ii] emission-line galaxies using the data from the second Public Data Release (PDR2) of the Subaru Strategic Program (SSP) of the HSC and Cosmic HydrOgen Reionization Unveiled with Subaru (CHORUS) survey along with the spectroscopic redshifts for 2019 emission-line galaxies selected with the PDR1 data. The wider effective coverage of NB816 and NB921, 16.3 deg2 and 16.9 deg2, respectively, are available in the Deep and UltraDeep layers of HSC-SSP from the PDR2. The CHORUS survey provides us with data with additional three NBs (NB527, NB718, and NB973) in the COSMOS field in the UltraDeep layer (1.37 deg2). The five NB datasets allow us to investigate the star-forming galaxies presenting emission-lines at 14 specific redshifts ranging from z ∼ 1.6 down to z ∼ 0.05. We revisit the distribution of large-scale structures and luminosity functions (LFs) for the emission-line galaxies with the large samples of 75377 emission-line galaxies selected. The redshift revolution of LFs shows that the star formation rate densities (SFRDs) decreases monotonically from z ∼ 1.6, which is consistent with the cosmic SFRD known to-date. Our samples of emission-line galaxies covering a sufficiently large survey volume are useful to investigate the evolution of star-forming galaxies since the cosmic noon in a wide range of environments including galaxy clusters, filaments, and voids.

Hayashi, Masao (ORCID:0000000293217406)↗

Localized growth and remodelling drives spongy mesophyll morphogenesis

The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll must develop from an initially confluent tissue into a tortuous network of cells with a large proportion of intercellular airspace. How the airspace in the spongy mesophyll develops while the tissue remains mechanically stable is unknown. Here, we use computer simulations of deformable polygons to develop a purely mechanical model for the development of the spongy mesophyll tissue. By stipulating that cell wall growth and remodelling occurs only near void space, our computational model is able to recapitulate spongy mesophyll development observed in Arabidopsis thaliana leaves. We find that robust generation of pore space in the spongy mesophyll requires a balance of cell growth, adhesion, stiffness and tissue pressure to ensure cell networks become porous yet maintain mechanical stability. The success of this mechanical model of morphogenesis suggests that simple physical principles can coordinate and drive the development of complex plant tissues like the spongy mesophyll.

Science & Technology - Other Topics↗

Uniaxial tensile mechanical properties from a scratch on ultra-fine grained tungsten

We demonstrate that surface-based mechanical testing can be used to quantify a wide range of mechanical properties determined using traditional uniaxial tension experiments. These include mapping of dynamic stress–strain behaviour, which can be used as a screening tool for uniaxial tensile ductility (uniform elongation), fracture toughness (K C ), which is shown to be in good agreement with reported plane-strain K IC , as well work-hardening exponents (n), activation volumes (V) energies (Q) and strain-rate sensitivity (m) exponents as a function of temperature. Advantages of the surface-based approach are the ability to work with significantly smaller volumes and accommodate processing defects like pores, voids and cracks. These methods are applied to ultra-fine grained tungsten (average grain size of 650 nm), as it is an ideal candidate for alloy development efforts in advanced energy systems. Tungsten is a useful baseline as it exhibits a near-ambient temperature (approx. 200°C) ductile-to-brittle transition temperature (DBTT), enabling validation efforts for the proposed methods, and extraordinary material properties, including the highest melting temperature of any metal and complex temperature and strain-rate dependencies linked to transitions in dislocation mechanisms.

36 MATERIALS SCIENCE↗

Subexponential Decay of Local Correlations from Diffusion-Limited Dephasing

Chaotic quantum systems at finite entropy density are expected to act as their own heat baths, rapidly dephasing local quantum superpositions. Here, we argue that in fact this dephasing is generically subexponential in one-dimensional systems with conservation laws: all local correlation functions decay as exp⁡[−𝒪⁡(𝑡 𝛼 )] with 0 ≤ 𝛼 ≤ 2/3, even when the operators are orthogonal to all hydrodynamic modes. The mechanism is diffusion-limited dephasing, in which rare low-entropy regions (“voids”) protect quantum coherences. This intrinsically quantum effect lies beyond standard hydrodynamics and disappears under extrinsic dephasing. In random charge-conserving circuits we find 𝛼 = 1/2, while in generic translation-invariant Floquet systems we bound 𝛼 ≤ 2/3. Our arguments are general, subject principally to the assumption that thermal fluctuations can create regions of zero entropy density. In systems with energy conservation, this assumption is automatically satisfied because of the third law of thermodynamics.

information scrambling↗

Passive Freeze-Out of the Richtmyer-Meshkov Instability

The Richtmyer-Meshkov instability (RMI) poses a major challenge in inertial confinement fusion (ICF) due to its role in mixing and performance degradation. We report the first experimental observation of passive freeze-out of RMI in a low-pressure surrogate regime, an instability stagnation effect induced without modifying the driving pressure pulse or the target surface geometry. Using additively manufactured subsurface voids in a sinusoidal target, we convert a single shock into a sequence of weaker shocks that suppress instability growth upstream of the surface by over 70%. High-speed x-ray imaging and hydrodynamic simulations suggest that this suppression arises primarily from temporal shaping, with lesser contributions from spatial curvature and shock weakening. Our results demonstrate a driver-independent pathway for controlling shock-driven hydrodynamic instabilities relevant to ICF and other high energy density systems.

Materials science↗

Resistivity anisotropy of quantum Hall stripe phases

In this work, quantum Hall stripe phases near half-integer filling factors $\nu$ $\geqslant$ 9/2 were predicted by Hartree-Fock (HF) theory and confirmed by discoveries of giant resistance anisotropies in high-mobility two dimensional electron gases. A theory of such anisotropy was proposed by MacDonald and Fisher, although they used parameters whose dependencies on the filling factor, electron density, and mobility remained unspecified. Here, we fill this void by calculating the hard-to-easy resistivity ratio as a function of these three variables. Quantitative comparison with experiment yields very good agreement, which we view as evidence for the “plain vanilla” smectic stripe HF phases

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Pressure-induced polyamorphic transition in CaA l 2 O 4 glass

In situ high-pressure ultrasonic velocity measurements of CaAl 2 O 4 glass reveal abrupt irreversible discontinuities in the elastic wave velocities at ~8–10 GPa. Total structure factor and pair distribution functions measured by synchrotron x-ray diffraction show a rapid change in the intermediate range structure attributed to a rearrangement of calcium ions over this narrow pressure region. Atomistic models obtained from molecular dynamics simulations reveal that this intermediate range structure is explained by a transition of Ca–O void radius distribution from a bimodal distribution with peaks at ~2.1 and ~2.4 Å to a single distribution centered at ~2.1 Å. Further, these abrupt structural changes involving the rapid increase in elastic wave velocity are markedly different to the continuous transformations observed in conventional network-forming glasses, such as SiO 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Can late dark energy transitions raise the Hubble constant?

Late times dark energy transitions at redshifts z << 0.1 can raise the predicted value of the Hubble constant to the SH0ES value, 74.03 ± 1.42 (km s –1 Mpc –1 ) or more, while providing an equally good fit as Λ CDM at 67.73±0.41 to higher redshift data, in particular from the cosmic microwave background and baryon acoustic oscillations. Here, these models however do not fully resolve the true source of tension between the distance ladder and high redshift observations: the local calibration of supernovae luminosities well out into the Hubble flow. When tested in this manner by transferring the SH0ES calibration to the Pantheon supernovae dataset, the ability of such transitions to raise the Hubble constant is reduced to 69.17 ± 1.09. Such an analysis should also be used when testing any dynamical dark energy model which can produce similarly fine features in redshift or local void models.

79 ASTRONOMY AND ASTROPHYSICS↗

Pressure dependence of intermediate-range order and elastic properties of glassy Baltic amber

Amber is a unique example of a fragile glass that has been extensively aged below its glass transition temperature, thus reaching a state that is not accessible under normal experimental conditions. In this paper, we studied the medium-range order of Baltic amber by x-ray diffraction (XRD) at high pressures. The pressure dependences of the low-angle XRD intensity between 0 and 5 Å -1 were measured from 0 to 7.3 GPa by the energy-dispersive XRD. The first diffraction peak at 1.1 Å -1 and ambient pressure has a doublet structure consisting of the first sharp diffraction peak (FSDP) at 1.05 Å -1 and the second feature at 1.40 Å -1 . The peak position and the width of the FSDP increase as the pressure increases, while the intensity of the FSDP decreases. Below P 0 = 2.4 GPa, the rapid increase of the FSDP peak position was observed, while above P 0 , the gradual increase was observed. Below P 0 , voids and holes in a relatively low-density state are suppressed, whereas above P 0 , the suppression becomes mild. Such a change suggests the crossover from the low- to high-density state at P 0 . There is a close correlation between the pressure dependence of XRD and previously reported sound velocity results. The correlation between the mean-square fluctuation of the shear modulus on the nanometer scale and fragility in amber and other glass formers is also discussed.

36 MATERIALS SCIENCE↗

Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here, in this work, we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

74 ATOMIC AND MOLECULAR PHYSICS↗

Connecting mechanical properties to hydrogen defects in PAN-based carbon fibers

Atomic-level defects dictate the mechanical properties of carbon fibers and strong correlations have been established between the crystallite sizes and mechanical properties. We recently demonstrated similar correlations with hydrogen content, but reliably quantifying the hydrogen content is not possible using only inelastic neutron scattering experiments. Here, we present prompt-gamma activation analysis (PGAA) experiments collected on 20 commercially available carbon fibers to quantify the hydrogen content of carbon fibers and find correlations between fiber modulus and hydrogen content. We then evaluate the role of hydrogen defect type and connect the PGAA results to both newly acquired and recently reported inelastic neutron scattering experiments. In conclusion, we find that intercalated hydrogen defects are preferentially removed at carbonization temperatures required for high-modulus fibers, potentially giving rise to voids within the carbon fibers that undermine their tensile strength.

36 MATERIALS SCIENCE↗

First-principles investigation of elastic, vibrational, and thermodynamic properties of kagome metals CsM 3 Te 5 (M = Ti, Zr, Hf)

Kagome metals are a unique class of quantum materials characterized by their distinct atomic lattice arrangement, featuring interlocking triangles and expansive hexagonal voids. These lattice structures impart exotic properties, including superconductivity, interaction-driven topological many-body phenomena, and magnetism, among others. The kagome metal CsM 3 ⁢Te 5 (where M = Ti, Zr, or Hf) exhibits both superconductivity and nontrivial topological electronic properties, offering a promising platform for exploring topological superconductivity. This study employs first-principles density functional theory calculations to systematically analyze the elastic, mechanical, vibrational, thermodynamic, and electronic properties of CsM 3 ⁢Te 5 (M = Ti, Zr, Hf). Our calculations reveal that the studied compounds—CsTi 3 ⁢Te 5 , CsZr 3 ⁢Te 5 , and CsHf 3 ⁢Te 5 —are ductile metals with elastic properties akin to the hexagonal Bi and Sb, with average elastic constants, including a bulk modulus of 27 GPa, a shear modulus of 11 GPa, and Young's modulus of 29 GPa. We observe peculiar dispersionless, flat, phonon branches in the vibrational spectra of these metals. Additionally, we thoroughly analyze the symmetries of the zone-center phonon eigenvectors and predict vibrational fingerprints of the Raman- and infrared-active phonon modes. The analysis of thermodynamic properties reveals the Einstein temperature for CsTi 3 ⁢Te 5 , CsZr 3 ⁢Te 5 , and CsHf 3 ⁢Te 5 to be 66, 54, and 53 K, respectively. Our orbital-decomposed electronic structure calculations reveal significant in-plane steric interactions and multiple Dirac band crossings near the Fermi level. We further investigate the role of spin-orbit coupling effect on the studied properties. Furthermore, this theoretical investigation sheds light on the intriguing quantum behavior of kagome metals.

36 MATERIALS SCIENCE↗

K-space algorithmic reconstruction (KAREN): a robust statistical methodology to separate Bragg and diffuse scattering

Diffuse scattering occurring in the Bragg diffraction pattern of a long-range-ordered structure represents local deviation from the governing regular lattice. However, interpreting the real-space structure from the diffraction pattern presents a significant challenge because of the dramatic difference in intensity between the Bragg and diffuse components of the total scattering function. In contrast to the sharp Bragg diffraction, the diffuse signal has generally been considered to be a weak expansive or continuous background signal. In this paper, using 1D and 2D models, it is demonstrated that diffuse scattering in fact consists of a complex array of high-frequency features that must not be averaged into a low-frequency background signal. To evaluate the actual diffuse scattering effectively, an algorithm has been developed that uses robust statistics and traditional signal processing techniques to identify Bragg peaks as signal outliers which can be removed from the overall scattering data and then replaced by statistically valid fill values. This method, described as a 'K-space algorithmic reconstruction' (KAREN), can identify Bragg reflections independent of prior knowledge of a system's unit cell. KAREN does not alter any data other than that in the immediate vicinity of the Bragg reflections, and reconstructs the diffuse component surrounding the Bragg peaks without introducing discontinuities which induce Fourier ripples or artifacts from underfilling `punched' voids. The KAREN algorithm for reconstructing diffuse scattering provides demonstrably better resolution than can be obtained from previously described punch-and-fill methods. The superior structural resolution obtained using the KAREN method is demonstrated by evaluating the complex ordered diffuse scattering observed from the neutron diffraction of a single plastic crystal of CBr 4 using pair distribution function analysis.

36 MATERIALS SCIENCE↗

Dynamic structural and microstructural responses of a metal–organic framework type material to carbon dioxide under dual gas flow and supercritical conditions

The structural and microstructural responses of a model metal–organic framework material, Ni(3-methyl-4,4'-bipyridine)[Ni(CN) 4 ] (Ni-BpyMe or PICNIC-21), to CO 2 adsorption and desorption are reported for in situ small-angle X-ray scattering and X-ray diffraction measurements under different gas pressure conditions for two technologically important cases. These conditions are single or dual gas flow (CO 2 with N 2 , CH 4 or H 2 at sub-critical CO 2 partial pressures and ambient temperatures) and supercritical CO 2 (with static pressures and temperatures adjusted to explore the gas, liquid and supercritical fluid regimes on the CO 2 phase diagram). The experimental results are compared with density functional theory calculations that seek to predict where CO 2 and other gas molecules are accommodated within the sorbent structure as a function of gas pressure conditions, and hence the degree of swelling and contraction in the associated structure spacings and void spaces. Furthermore, these predictions illustrate the insights that can be gained concerning how such sorbents can be designed or modified to optimize the desired gas sorption properties relevant to enhanced gas recovery or to addressing carbon dioxide reduction through carbon mitigation, or even direct air capture of CO 2 .

36 MATERIALS SCIENCE↗

Crystal structure of a trigonal polymorph of aquadioxidobis(pentane-2,4-dionato-κ 2 O , O ′)uranium(VI)

The title compound, [UO 2 (acac) 2 (H 2 O)] consists of a uranyl(VI) unit ([O=U=O] 2+ ) coordinated to two monoanionic acetylacetonate (acac, C 5 H 7 O 2 ) ligands and one water molecule. The asymmetric unit includes a one-half of a uranium atom, one oxido ion, one-half of a water molecule and one acac ligand. The coordination about the uranium atom is distorted pentagonal–bipyramidal. The acac ligands and O w atom comprise the equatorial plane, while the uranyl O atoms occupy the axial positions. Intermolecular hydrogen bonding between complexes results in the formation of two-dimensional hexagonal void channels along the c- axis direction with a diameter of 6.7 Å. The monoclinic ( P 2 1 / c space group) polymorph was reported by Alcock & Flanders [(1987). Acta Cryst. C 43 , 1480–1483].

Hernandez, Alejandro↗

Structural characterization of a new samarium–sodium heterometallic coordination polymer

Lanthanide-containing materials are of interest in the field of crystal engineering because of their unique properties and distinct structure types. In this context, a new samarium–sodium heterometallic coordination polymer, poly[tetrakis(μ 2 -2-formyl-6-methoxyphenolato)samarium(III)sodium(I)], {[SmNa(C 8 H 7 O 3 ) 4 ]·solvent} n ( Sm-1 ), was synthesized and crystallized via slow evaporation from a mixture of ethanol and acetonitrile. The compound features alternating Sm III and Na I ions, which are linked by ortho -vanillin ( o -vanillin) ligands to form a mono-periodic chain-like coordination polymer. The chains propagate along the [001] direction. Residual electron density of disordered solvent molecules in the void space could not be reasonably modeled, thus the SQUEEZE function was applied. The structural, vibrational, and optical properties are reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗