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At least 415 records · Page 23

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Background Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood. Results Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H 3 K 4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains. Conclusions Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

59 BASIC BIOLOGICAL SCIENCES↗

Radar transmit bandwidth augmentation

Various technologies pertaining to forming a very high instantaneous bandwidth (IBW) radar signal based upon several radio frequency (RF) signals that have sub-bands of the frequency band of the radar signal are described herein. A radar system is configured to address local oscillator leakage across multiple transmit channels of the radar system, such that the radar signal has a relatively constant or other desired amplitude and phase across frequencies of the radar signal. In addition, the radar system is configured to compute a correction signal that pre-distorts each of the sub-frequency channels such that upon combining enables the generation of desired amplitude and phase response across a transmitted pulse.

Loui, Hung↗

Octahedral to tetrahedral bonding transitions in the local structure of phase change optical media Ge 2 Sb 2 Se 5 x Te 5-5 x with Se doping

Random access memories utilize fast, reversible switching between ordered and disordered states of matter in phase change materials (PCMs) such as Ge2Sb2Te5-5x. The short-range structure in the disordered phase has been described either as (i) a network of Ge tetrahedra or (ii) Peierls distorted Ge/Sb octahedra. The PCM transition was investigated in bulk Ge2Sb2Se5xTe5-5x (GSST), in which amorphization sets in with Se doping (x ≈ 0.85) upon quenching. GSST has a hexagonal crystalline ground state with Ge/Sb octahedral coordination, but the phase change transition to the amorphous state that is only observed when the system is quenched brings a short-range structure with sharp, tetrahedrally coordinated Ge/Sb correlations and shortened bonds that are distinctly different from the expected octahedral pairing.

97 MATHEMATICS AND COMPUTING↗

Electronic Excitation‐Driven β‐Ga 2 O 3 Metastability Transformation and Self‐Organization Mechanism: β→κ/γ/δ Phases

Here, irradiation-driven multiphase self-organization presents emergent opportunities for the customization of nanoscale engineering properties, dynamically tuning strain-field distributions and interfacial electronic structures. Responding to intense electronic excitation-induced energy deposition, the dominant phase transformations, with varying Gibbs free energy $Δ,G^o_f$ are confirmed as β → κ → γ → δ that are located in specific microregions for Gallium (III) oxide (Ga 2 O 3 ), as follows: (i) Surface-localized interstitial accumulation under compressive stress triggers β → δ via semi-coherent interface formation. (ii) Tensile stress within latent tracks drives vacancy-mediated oxygen layer truncation (4/12 periodicity along ⟨0001⟩), stabilizing coherent 4H (ABCB) κ and 3C (ABC) β (ABC) interfaces through strain-compensated octahedral distortion. (iii) Screw dislocation-mediated lattice relaxation induces β → γ via cation disordering (Ga 3+ occupancy at β-interstitial sites), forming metastable spinel γ with mixed occupancy across 16d/8a Wyckoff sites. Irradiation-driven β-Ga 2 O 3 →κ/γ/δ transitions, as mechanistically revealed via inelastic thermal spike (i-TS) calculations and molecular dynamics simulations, induce defect-mediated nonlinear photoresponse, critical for optoelectronic engineering.

Han, Xinqing [Shandong Univ., Jinan (China)]↗

Determining Stress in Metallic Conducting Layers of Microelectronics Devices Using High Resolution Electron Backscatter Diffraction and Finite Element Analysis

Delayed failure due to stress voiding is a concern with some aging microelectronics, as these voids can grow large enough to cause an open circuit. Local measurements of stress in the metallic layers are crucial to understanding and predicting this failure, but such measurements are complicated by the fact that exposing the aluminum conducting lines will relieve most of their stress. In this study, we instead mechanically thin the device substrate and measure distortions on the thinned surface using high resolution electron backscatter diffraction (HREBSD). These measurements are then related to the stresses in the metallic layers through elastic simulations. This study found that in legacy components that had no obvious voids, the stresses were comparable to the theoretical stresses at the time of manufacture (≈300 MPa). Distortion fields in the substrate were also determined around known voids, which may be directly compared to stress voiding models. In conclusion, the technique presented here for stress determination, HREBSD coupled with finite element analysis to infer subsurface stresses, is a valuable tool for assessing failure in layered microelectronics devices.

HREBSD↗

Defect-induced electronic smectic state at the surface of nematic materials

Due to the intertwining between electronic nematic and elastic degrees of freedom, lattice defects and structural inhomogeneities commonly found in crystals can have a significant impact on the electronic properties of nematic materials. Here, we show that defects commonly present at the surface of crystals generally shift the wave-vector of the nematic instability to a non-zero value, resulting in an incommensurate electronic smectic phase. Such a smectic state onsets above the bulk nematic transition temperature and is localized near the surface of the sample. We argue that this effect may explain not only recent observations of a modulated nematic phase in iron-based superconductors, but also several previous puzzling experiments that reported signatures consistent with nematic order before the onset of a bulk structural distortion.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Geometric Interpretation of the Cluster Location Problem Part I: Theory

We present a new framing of the seismic location problem using principles drawn from differential geometry. Our interpretation relies upon the common assumption that travel times observed across a network are continuous, differentiable functions of source location. In consequence, travel‐time functions constitute a differentiable map between the source region and a Riemannian manifold. The manifold is said to be the image of the source region embedded in a generally high‐dimension travel‐time vector space. A cluster of events in the source region has an image of discrete points on the manifold, that, except in the simplest cases, cannot be viewed directly. However, it is possible to project the image of a cluster into a tangent space of the manifold for direct visualization. The projection operator can be computed directly from the data without a velocity model, but produces a distorted rendering of the cluster geometry. With a model we can predict the distortions and correct them to estimate cluster geometry. We develop these points with the simplest possible example, one for which direct visualization of the manifold is possible, using the example as an introduction to the relevant concepts from differential geometry in a familiar setting. The tangent space, a local linearization of the manifold, plays a key role. We develop a metric to estimate the limits of linearization, that is, to determine when the curvature of the manifold invalidates the linear assumption. We also examine the interplay of model error, inadequate network geometry, and pick error. We then generalize our results from the simple case to the general case of 3D source regions observed by general networks. Although we do suggest a new “project and correct” method for location, we do not develop it into a practical algorithm. In conclusion, our intention rather is to highlight new analytical methods grounded in differential geometry.

East Pacific Ocean Islands↗

Machine Learning Vacancy Formation Energy in Nickel-Based Superalloys

Thermal vacancies play a critical role in high-temperature Ni-based superalloys and influence various properties such as creep resistance, oxidation, etc. This study systematically investigates the impact of commonly used transition metals (Cr, Co, Fe), refractory metals (Nb, Ta, Mo, W) and other elements (Al, Cu, Ti, Mn) on the thermodynamic stability of 36 binary, 20 ternary, 11 quaternary, 9 quinary, and 3 senary FCC Ni-based alloys covering various elemental combinations. Density functional theory-based studies on Ni-X binary alloys show that higher concentrations of Cr, Nb, Ta, Al, and Ti introduce significant lattice distortions and broaden the distribution of vacancy formation energies (standard deviation up to 0.15 eV). These elements partially donate electrons, reducing their self-consistent chemical potentials relative to single-element reference values and lowering vacancy formation energies, while Co, Fe, Mo, and W show lower charge localization. These trends extend from 3-6 element alloys, where Cr, Nb, and Ta-rich compositions have low-energy states (~0.5 eV) that increase vacancy concentrations. Finally, graph neural network models are developed to screen over 5000 virtual alloys. Eleven leading compositions are identified with mean vacancy formation energy higher than 1.75 eV and vacancy concentration ~2 orders of magnitude lower than pure Ni at 1000 K. These results provide valuable guidelines to achieve controlled defect engineering in structural alloys.

DFT↗

Pressure tuning of Kitaev spin liquid candidate Na$_3$Co$_2$SbO$_6$goo

The search for Kitaev's quantum spin liquid (KQSL) state in real materials has recently expanded with the prediction that honeycomb lattices of divalent, high-spin cobalt ions could host the dominant bond-dependent exchange interactions required to stabilize the elusive entangled quantum state. The layered honeycomb Na$_3$Co$_2$SbO$_6$ has been singled out as a leading candidate provided that the trigonal crystal field acting on Co $3d$ orbitals, which enhances non-Kitaev exchange interactions between $J_{\rm eff}=\frac{1}{2}$ spin-orbital pseudospins, is reduced. We find that applied pressure leads to anisotropic compression of the layered structure, significantly reducing the trigonal distortion of CoO$_6$ octahedra. A strong enhancement of ferromagnetic correlations between pseudospins is observed in the spin-polarized (3 Tesla) phase up to about 60 GPa. Higher pressures drive a spin transition into a low-spin state destroying the $J_{\rm eff}=\frac{1}{2}$ local moments required to map the spin Hamiltonian into Kitaev's model. The spin transition strongly suppresses the low-temperature magnetic susceptibility and appears to stabilize a paramagnetic phase driven by frustration. Although applied pressure fails to realize a KQSL state, the possible emergence of frustrated magnetism of localized, low-spin $S=\frac{1}{2}$ moments opens the door for exploration of novel magnetic quantum states in compressed honeycomb lattices of divalent cobaltates.

FOS: Physical sciences↗

Comparison of Results between the Legacy and Refined RELAP5-3D Models of the High Temperature Test Facility in Exercises 1 and 2 of the HTTF Benchmark

Work conducted in FY23 identified that RELAP5-3D was capable of reproducing trends in HTTF data during experiment PG-27 but was incapable of reproducing measured values. The primary cause of this discrepancy between RELAP5-3D results and experimental data was hypothesized to be a distortion in power density that was introduced by the radial nodalization of the model. We further hypothesized that a new model would provide better results when compared to the experiments PG-27 and PG-29. Work this FY developed a new model that is better capable of capturing local heat generation rates and contains a representation of each 1/6 azimuthal sector of the core. We used this model to develop a new set of solutions to Exercises 1 and 2 of Problems 2 and 3 in the benchmark. In this report, we present the first comprehensive comparison of the results between the two models. We see that in Exercise 1A, which is common between problems 2 and 3, the results are similar, though the results from the new model show greater detail than those from the legacy model. In Problem 2 Exercise 1B and Problem 3 Exercise 1B, we see that heat removal is slower in the new model than the legacy model. Problem 3 Exercise 1C shows temperatures that are lower in most places in the new model than the legacy model, but the area with active heat generation has higher block temperatures in the new model than the legacy model. Problem 3 Exercise 1D further shows that long-term heat removal is lower in the new model. Problem 2 Exercise 1C demonstrated that the new model observes higher temperatures in the core regions than the legacy model, justifying the need to preserve the power density in HTTF. The validation of PG-27 and PG-29 also demonstrated the improved temperature agreement in the core regions, particularly with a calibrated model that implements an effective thermal conductivity for the core material. Overall, PG-27 models show reasonable to excellent agreement for steady-state temperatures and minimal to reasonable agreement for transients. PG-29 models showed minimal to insufficient agreement with the data.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Single-shot local measurement of terahertz correlated second harmonic generation in laser air plasma filaments

We present a single-shot detection method of terahertz correlated second harmonic generation in plasma-based sources by directly mixing an optical probe into femtosecond laser-induced plasma filaments in air. Furthermore, the single-shot second harmonic trace is obtained by measuring a second harmonic generation on a conventional CCD with a spatiotemporally distorted probe beam. The system shows a spectrometer resolution of 22 fs/pixel on the CCD and a true resolution on the order of the probe pulse duration. With considerable THz peak electric field strength, this formalism can open the door to single-shot THz detection without bandwidth limitations.

47 OTHER INSTRUMENTATION↗

Calibration of the ProtoDUNE Horizontal-Drift position reconstruction using a laser system

Forthcoming in the next decade of neutrino physics advancements is the construction of the Deep Underground Neutrino Experiment (DUNE), a long baseline neutrino oscillation experiment which has the potential to answer fundamental questions such as why there is more matter than antimatter in the universe, and ultimately why we exist at all. A prototype of this experiment, ProtoDUNE, sits in a charged particle test beam at the European Organization for Nuclear Research (CERN) and uses Liquid Argon time projection chambers to image interactions of these particles. ProtoDUNE Single-Phase (ProtoDUNESP) had positively charged hadrons as well as positrons in its initial 2018 beam data run. Because ProtoDUNE is a surface-based time projection chamber, it experiences a constant influx of cosmic rays. These cosmic rays ionize the liquid argon within the detector, resulting in an accumulation of slow moving positive ions towards the cathode. This local charge distribution results in electric field non uniformities, which can have a significant effect on the accuracy of the event reconstruction. This paper outlines a monte carlo simulation study which adapts methodology from the MicroBooNE experiment, another neutrino oscillation experiment, to derive electric field correction maps which can correct for distortions of the electric field within the detector. These correction maps accurately estimate the electric field throughout the detector volume and correct for uncertainties in reconstructed event data enabling for physics discoveries.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Unraveling the Nature of Vibrational Dynamics in CsPbI 3 by Inelastic Neutron Scattering and Molecular Dynamics Simulations

Cesium lead iodide, CsPbI 3 , is an optoelectronic material of large interest for various technological applications; however, fundamental questions surrounding the vibrational dynamics of this material, especially regarding its role in structural phase transitions, remain to be elucidated. Here, in a combined variable temperature inelastic neutron scattering (INS) and machine-learning based molecular dynamics (MD) simulation study, we show that the stable phase at room temperature, i.e., the nonperovskite δ-phase, exhibits phonon modes with weak anharmonicity with only a weak temperature dependence from 10 K all the way up to the transition to the cubic perovskite α-phase at approximately 600 K. In contrast, the α-phase features anharmonic and damped vibrational dynamics, mainly associated with overdamped tilting motions of the PbI 6 octahedra. Crucially, these overdamped tilting modes, which relate to the tetragonal and orthorhombic distorted perovskite phases (β- and γ-phase, respectively) formed at lower temperatures, stay overdamped by more than 100 K above the respective phase transition. This suggests a flat energy landscape of octahedral tilting motions in α-CsPbI3 and with structural fluctuations on the picosecond time scale with tilting patterns that locally resemble the structure of the β- and γ-phases. The vibrational dynamics of α-CsPbI 3 are also characterized by pronounced anharmonic motions with large thermal displacements of the Cs + ions, but these modes remain underdamped at 600 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ChemEnv : a fast and robust coordination environment identification tool

Coordination or local environments have been used to describe, analyze and understand crystal structures for more than a century. Here, a new tool called ChemEnv, which can identify coordination environments in a fast and robust manner, is presented. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen package and the software can also be used through a web app available on http://crystaltoolkit.org through the Materials Project.

42 ENGINEERING↗

A small-box approach to the local crystal structure of Y 3 NbO 7

The local crystal structure of Y 3 NbO 7 was probed using neutron total scattering. Five different structural models were fit to the experimental pair distribution function of this material up to 15 Å. Fits of defect fluorite (Fm$\overline{3}$m), pyrochlore (Fd$\overline{3}$m), and orthorhombic C weberite models (C222 1 ) were attempted based on prior structural investigations of Y 3 NbO 7 and related fluorite-based materials. Orthorhombic P weberite (P222 1 ) and monoclinic weberite models (P112 1 ) were derived via symmetry reduction of the orthorhombic C weberite structure. All models except monoclinic weberite failed to reproduce the experimental pair distribution function. Misfits were clearly visible for peaks arising from atom pairs within the first coordination shell (defect fluorite and pyrochlore) and beyond (orthorhombic C and P weberite). By contrast, monoclinic weberite (γ ≈ 91.8°) provided an excellent fit, with no major misfits observed. This unit cell features distorted YO 8 dodecahedra, YO 7 monocapped octahedra, and NbO 6 octahedra as building blocks. Comparison between the topologies of the cationic and anionic substructures in monoclinic weberite and its parent orthorhombic C structure revealed displacements of the metal atoms along the [100] direction and a less compact spatial distribution of oxygen atoms along the a axis. In conclusion, the monoclinic weberite model presented herein may serve as a starting point to revisit structural modeling of fluorite-based materials with challenging local structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanoscopic strain evolution in single-crystal battery positive electrodes

Single-crystal Ni-rich layered oxides (SC-NMC) with a grain-boundary-free configuration have effectively addressed the long-standing cracking issue of conventional polycrystalline Ni-rich materials (PC-NMC) in lithium-ion batteries, prompting a shift in optimization strategies. However, continued reliance on anisotropic lattice volume change—a well-established failure indicator in PC-NMC—as a metric for understanding strain and guiding compositional design for SC-NMC becomes controversial. Here, in this study, by leveraging multiscale diagnostic techniques, we unravelled the distinct nanoscopic strain evolution in SC-NMC during battery operation, challenging the conventional composition-driven strategies and mechanical degradation indicators used for PC-NMC. Through particle-level chemomechanical analysis, we reveal a decoupling between mechanical stability and lattice volume change in SC-NMC, identifying that structural instability in SC materials is primarily driven by multidimensional lattice distortions induced by kinetics-driven reaction heterogeneity and progressively deactivating chemical phases. Using this mechanical failure mode, we redefine the roles of cobalt and manganese in maintaining mechanical stability. Unlike cobalt’s detrimental role in PC-NMC, we find cobalt to be critical in enhancing the longevity of SC-NMC by mitigating localized strain along the extended diffusion pathway, whereas manganese exacerbates mechanical degradation.

36 MATERIALS SCIENCE↗

Hierarchy among the crystal lattice, charge density wave, and superconducting orders in transition metal dichalcogenides

Using high-energy x-ray scattering and large-scale three-dimensional (3D) structure modeling, in this study we investigate the relationship between the crystal lattice, charge density wave (CDW), and superconducting (SC) orders in transition metal dichalcogenides (TMDs). In particular, we systematically substitute Te for Se in Ta-Se-Te solid solutions, determine changes in their crystal lattice, and relate them to changes in the CDW transition temperature, $T_{CDW}$, and SC critical temperature, $T_c$ . We find that strong lattice distortions such as buckling of Ta layers are detrimental to the CDW and SC orders. The presence of a perfect lattice order in two dimensions is a prerequisite to the emergence of CDWs but insufficient to achieve a SC ordered state. For the SC order to emerge, the Ta sublattice should also appear periodic in 3D. Local chemical disorder may promote the SC order, and the perfectness of Ta coordination polyhedra is a factor contributing to its strength. A hierarchical relationship among the crystal lattice, CDW, and SC orders thus appears to exist in TMDs in a sense that different degrees of crystal lattice order-disorder promote and maintain the CDW and SC orders to a different extent, offering an opportunity to control the latter through modifying the former by rational design. Our findings are a step towards a better understanding of the correlation between lattice and electronic degrees of freedom in TMDs. We also demonstrate an efficient experimental approach to study them in fine detail.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗