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At least 469 records · Page 26

Identification of KLHL12 Ligands Using Fragment-Based Methods

Targeted protein degradation can be induced by recruiting a protein of interest to an E3 ligase, resulting in its ubiquitination and subsequent proteasome-mediated degradation. However, only a small number of E3 ligases have been utilized for degradation. Expansion of the repertoire of useful E3 ligases via the identification of ligands to those ligases could broaden the scope and applicability of the degradation paradigm. We have identified KLHL12 as an E3 ligase with higher expression in cancer over normal tissues. We report here the use of NMR-based screening to identify fragments that bind to KLHL12, and X-ray structures of a fragment hit bound to KLHL12. Using this structural information, we optimized the hits, leading to the first reported small molecules that bind to KLHL12 with submicromolar affinity. Derivatives of these compounds may be useful for the construction of PROTACs to selectively degrade protein targets in tumors while sparing normal cells.

Amines↗

Methane Adsorption on Heteroatom-Modified Maquettes of Porous Carbon Surfaces

Experimental and theoretical studies disagree on the energetics of methane adsorption on carbon materials. However, this information is critical for the rational design and optimization of the structure and composition of adsorbents for natural gas storage. The delicate nature of dispersion interactions, polarization of both the adsorbent and the adsorbate, interplay between H-bonding and tetrel bonding, and induced dipole/Coulomb interactions inherent to methane physisorption require computational treatment at the highest possible level of theory. In this study, we employed the smallest reasonable computational model, a maquette of porous carbon surfaces with a central site for substitution and methane binding. The most accurate predictions of methane adsorption energetics were achieved by electron-correlated molecular orbital theory CCSD(T) and hybrid density functional theory MN15 calculations employing a saturated, all-electron basis set. Here, the characteristic geometry of methane adsorption on a carbon surface (“lander approach”) arises due to bonding interactions of the adsorbent π-system with the proximal H–C bonds of methane, in addition to tetrel bonding between the antibonding orbital of the distal C–H bond and the central atom of the maquette (C, B, or N). The polarization of the electron density, structural deformations, and the comprehensive energetic analysis clearly indicate a ∼3 kJ mol –1 preference for methane binding on the N-substituted maquette. The B-substituted maquette showed a comparable or lower binding energy than the unsubstituted, pure C model, depending on the level of theory employed. The calculated thermodynamic results indicate a strategy for incorporating electron-enriched substitutions (e.g., N) into carbon materials as a way to increase methane storage capacity over electron-deficient (e.g., B) modifications. The thermochemical analysis was revised for establishing a conceptual agreement between the experimental isosteric heat of adsorption and the binding enthalpies from statistical thermodynamics principles.

03 NATURAL GAS↗

Elucidating Compositional Differences in Halide Perovskites for Normal and Inverted Perovskite Solar Cells

Over the recent few years, extensive research efforts have shifted from normal (n-i-p) to inverted (p-i-n) perovskite solar cells (PSCs), owing to their promising efficiency and operational stability, enabled by low-temperature processing. Despite a fundamentally identical operation principle (only structurally inverted), the optimized perovskite compositions for normal and inverted PSCs differ significantly across the literature, suggesting an underlying design principle for perovskite composition. Here, we unveil the role of cesium cation in enhancing interfacial contact between the perovskite layer and the underlying hole-transporting layer (HTL) in inverted PSCs. Comprehensive in situ and device characterization reveal that cesium incorporation promotes the formation of initial nucleation seeds for heterogeneous nucleation at the perovskite/hydrophobic HTL interface, thereby improving their contact. The resulting compositional heterogeneity explains the focus of recent studies on resolving this issue. This study provides mechanistic insight into designing perovskite compositions to further enhance the performance and longevity of PSCs.

Park, Keonwoo↗

Systematic determination of a material’s magnetic ground state from first principles

Abstract We present a self-consistent method based on first-principles calculations to determine the magnetic ground state of materials, regardless of their dimensionality. Our methodology is founded on satisfying the stability conditions derived from the linear spin wave theory (LSWT) by optimizing the magnetic structure iteratively. We demonstrate the effectiveness of our method by successfully predicting the experimental magnetic structures of NiO, FePS 3 , FeP, MnF 2 , FeCl 2 , and CuO. In each case, we compared our results with available experimental data and existing theoretical calculations reported in the literature. Finally, we discuss the validity of the method and the possible extensions.

Chemistry↗

De novo design of pH-responsive self-assembling helical protein filaments

Abstract Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

3D-printed micro ion trap technology for quantum information applications

Trapped-ion applications, such as in quantum information processing1, precision measurements, optical clocks and mass spectrometry, rely on specialized high-performance ion traps. The last three of these applications typically use traditional machining to customize macroscopic 3D Paul traps, whereas quantum information processing experiments usually rely on photolithographic techniques to miniaturize the traps and meet scalability requirements. Using photolithography, however, it is challenging to fabricate the complex 3D electrode structures required for optimal confinement. Here, in this work, we demonstrate a high-resolution 3D printing technology based on two-photon polymerization (2PP) that is capable of fabricating large arrays of high-performance miniaturized 3D traps. We show that 3D-printed ion traps combine the advantages, such as strong radial confinement, of traditionally machined 3D traps with on-chip miniaturization. We trap calcium ions in 3D-printed ion traps with radial trap frequencies ranging from 2 MHz to 24 MHz. The tight confinement eases ion cooling requirements and allows us to implement high-quality Rabi oscillations with Doppler cooling only. Also, we demonstrate a two-qubit gate with a Bell-state fidelity of 0.978 ± 0.012. With 3D printing technology, the design freedom is greatly expanded without sacrificing scalability and precision, so that ion trap geometries can be optimized for higher performance and better functionality.

quantum information↗

Golden ratio in venation patterns of dragonfly wings

Abstract The vein pattern in insect wings allows this lightweight structure to carry multiple biological functions. Here, an investigation of the angular distribution of the vein struts in dragonfly wings revealed that the golden angle or golden ratio dominates the venation patterns. We find that the golden angle dominates the intervein angles in regions where thin veins and membranes demand strength reinforcement. A golden ratio partition method has thus been developed that explains a set of preferred intervein angles in distorted polygon-shaped venation cells throughout the venation pattern in dragonfly wings. These observations provide new evidence that the wing structure is spatially optimized, by the golden rule in nature, for supporting biomechanical functions of dragonfly wings.

36 MATERIALS SCIENCE↗

Printing thermoelectric inks toward next-generation energy and thermal devices

The ability of thermoelectric (TE) materials to convert thermal energy to electricity and vice versa highlights them as a promising candidate for sustainable energy applications. Despite considerable increases in the figure of merit zT of thermoelectric materials in the past two decades, there is still a prominent need to develop scalable synthesis and flexible manufacturing processes to convert high-efficiency materials into high-performance devices. Scalable printing techniques provide a versatile solution to not only fabricate both inorganic and organic TE materials with fine control over the compositions and microstructures, but also manufacture thermoelectric devices with optimized geometric and structural designs that lead to improved efficiency and system-level performances. In this review, we aim to provide a comprehensive framework of printing thermoelectric materials and devices by including recent breakthroughs and relevant discussions on TE materials chemistry, ink formulation, flexible or conformable device design, and processing strategies, with an emphasis on additive manufacturing techniques. Additionally, we review recent innovations in the flexible, conformal, and stretchable device architectures and highlight state-of-the-art applications of these TE devices in energy harvesting and thermal management. Perspectives of emerging research opportunities and future directions are also discussed. While this review centers on thermoelectrics, the fundamental ink chemistry and printing processes possess the potential for applications to a broad range of energy, thermal and electronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Measurement of femtosecond dynamics of ultrafast electron beams through terahertz compression and time-stamping

Visualizing ultrafast dynamics at the atomic scale requires time-resolved characterization with femtosecond temporal resolution. For fully relativistic electron bunch probes, existing techniques for single-shot ultrafast electron diffraction (UED) are limited by the achievable electron probe bunch length, charge, and timing jitter. We present the first experimental demonstration of dual-fed THz-driven compression and time-stamping that enables electron probes with improved temporal resolution. This technique utilizes two counter-propagating quasi-single-cycle THz pulses generated from two OH-1 organic crystals coupled into an optimized THz compressor structure. We demonstrate electron bunch compression and time-of-arrival jitter suppression by a factor of 3 paving the way toward unique opportunities for UED time-resolved measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Distributed memory, GPU accelerated Fock construction for hybrid, Gaussian basis density functional theory

With the growing reliance of modern supercomputers on accelerator-based architecture such a graphics processing units (GPUs), the development and optimization of electronic structure methods to exploit these massively parallel resources has become a recent priority. While significant strides have been made in the development GPU accelerated, distributed memory algorithms for many modern electronic structure methods, the primary focus of GPU development for Gaussian basis atomic orbital methods has been for shared memory systems with only a handful of examples pursing massive parallelism. Here in this work, we present a set of distributed memory algorithms for the evaluation of the Coulomb and exact exchange matrices for hybrid Kohn–Sham DFT with Gaussian basis sets via direct density-fitted (DF-J-Engine) and seminumerical (sn-K) methods, respectively. The absolute performance and strong scalability of the developed methods are demonstrated on systems ranging from a few hundred to over one thousand atoms using up to 128 NVIDIA A100 GPUs on the Perlmutter supercomputer.

97 MATHEMATICS AND COMPUTING↗

Growth and characterization of homoepitaxial β-Ga 2 O 3 layers

ß-Ga 2 O 3 is a next-generation ultra-wide bandgap semiconductor (E g = 4.8 eV to 4.9 eV) that can be homoepitaxially grown on commercial substrates, enabling next-generation power electronic devices among other important applications. Analyzing the quality of deposited homoepitaxial layers used in such devices is challenging, in part due to the large probing depth in traditional x-ray diffraction (XRD) and also due to the surface-sensitive nature of atomic force microscopy (AFM). Here, a combination of evanescent grazing-incidence skew asymmetric XRD and AFM are investigated as an approach to effectively characterize the quality of homoepitaxial ß-Ga 2 O 3 layers grown by molecular beam epitaxy at a variety of Ga/O flux ratios. Accounting for both structure and morphology, optimal films are achieved at a Ga/O ratio of ~1.15, a conclusion that would not be possible to achieve by either XRD or AFM methods alone. Finally, fabricated Schottky barrier diodes with thicker homoepitaxial layers are characterized by J-V and C-V measurements, revealing an unintentional doping density of 4.3×10 16 cm -3 - 2×10 17 cm -3 in the epilayer. These results demonstrate the importance of complementary measurement methods for improving the quality of the ß-Ga 2 O 3 homoepitaxial layers used in power electronic and other devices.

36 MATERIALS SCIENCE↗

Twelve-crystal prototype of Li 2 MoO 4 scintillating bolometers for CUPID and CROSS experiments

An array of twelve 0.28 kg lithium molybdate (LMO) low-temperature bolometers equipped with 16 bolometric Ge light detectors, aiming at optimization of detector structure for CROSS and CUPID double-beta decay experiments, was constructed and tested in a low-background pulse-tube-based cryostat at the Canfranc underground laboratory in Spain. Performance of the scintillating bolometers was studied depending on the size of phonon NTD-Ge sensors glued to both LMO and Ge absorbers, shape of the Ge light detectors (circular vs. square, from two suppliers), in different light collection conditions (with and without reflector, with aluminum coated LMO crystal surface). The scintillating bolometer array was operated over 8 months in the low-background conditions that allowed to probe a very low, μBq/kg, level of the LMO crystals radioactive contamination by 228 Th and 226 Ra.

47 OTHER INSTRUMENTATION↗

American cities in a time of global environmental change: the case of the Baltimore Social-Environmental Collaborative

The Baltimore Social-Environmental Collaborative (BSEC) Urban Integrated Field Laboratory seeks a new paradigm for urban climate research. Motivated by deep uncertainties in urban climate and the future of urban systems, BSEC works collaboratively across institutions and stakeholder groups to co-generate the science needed to advance energy security and resilience to extreme events across the city of Baltimore, Maryland, USA, and to do so in a manner that can inform similar efforts in other cities. BSEC begins with stakeholder priorities (health, affordable energy, etc) and designs observation networks and models to deliver climate science to address them. This takes the form of an iterative collaborative cycle, in which an initial research strategy is repeatedly updated in conversation with community partners, and researchers and stakeholders learn from each other. To date, this cycle has included multiple rounds of collaborative deliberation on urban heat mitigation, in which a multicriteria decision tool has been updated with more community-relevant spatial structure and modified optimization metrics. The guiding objective of this cycle is to inform potential ‘secure and resilient pathways’ for energy and infrastructure. In doing so, BSEC addresses fundamental urban science questions in natural and social sciences. It also tests our ability to integrate this science in a manner that advances participatory decision-making for urban resilience.

climate↗

Radial–axial transport coordination enhances sugar translocation in the phloem vasculature of plants

Abstract Understanding mass transport of photosynthates in the phloem of plants is necessary for predicting plant carbon allocation, productivity, and responses to water and thermal stress. Several hypotheses about optimization of phloem structure and function and limitations of phloem transport under drought have been proposed and tested with models and anatomical data. However, the true impact of radial water exchange of phloem conduits with their surroundings on mass transport of photosynthates has not been addressed. Here, the physics of the Munch mechanism of sugar transport is re-evaluated to include local variations in viscosity resulting from the radial water exchange in two dimensions (axial and radial) using transient flow simulations. Model results show an increase in radial water exchange due to a decrease in sap viscosity leading to increased sugar front speed and axial mass transport across a wide range of phloem conduit lengths. This increase is around 40% for active loaders (e.g. crops) and around 20% for passive loaders (e.g. trees). Thus, sugar transport operates more efficiently than predicted by previous models that ignore these two effects. A faster front speed leads to higher phloem resiliency under drought because more sugar can be transported with a smaller pressure gradient.

58 GEOSCIENCES↗

Spatial nematic fluctuation in BaFe 2 (As 1-x P x ) 2 revealed by spatially and angle-resolved photoemission spectroscopy

Nematicity, where rotational symmetry is broken while translational symmetry is conserved, is prevalent in higherature superconductors. In particular, nematic quantum critical point has been universally found near the optimum doping of the superconducting dome of several iron-based superconductor families. In such a regime, evidence for strong nematic fluctuations have been observed. As the precursor to this order, nematic fluctuations emerge before nematicity, providing favorable ground to study how nematic order modifies the electronic structure in the absence of structural distortion. Here we use spatially resolved angle-resolved photoemission spectroscopy to investigate the correlation between the onset of nematic fluctuations and electronic structure in an optimally doped BaFe 2 (As 1-x P x )2 (x ~ 0.3) superconductor. We reveal a strong spatially varying anisotropy of the Fermi surface on a length scale of tens of microns with strong correlation between the changes in the hole and electron Fermi pockets, consistent with the variations expected in the presence of fluctuating nematic order. These results provide direct evidence for spatial nematic fluctuations in the optimal doping regime of iron-based superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Role of Azimuthal Prestress in the Longitudinal Degradation of Nb 3 Sn Superconducting Magnets

Superconducting magnet coils are subject to enormous electro-magnetic forces which push the cables away from the winding pole, and against the surrounding structure. This structure is usually optimized trying to limit the overall motion and the strains experienced by the superconducting elements. To achieve this, preload forces are applied both in the coil cross-section and along its length. If the e.m. forces overcome these preloads, separation between the coil and the pole occurs, resulting in an overall loss of rigidity. During the magnet design process, it is often tempting to treat the optimization of the azimuthal and longitudinal preload systems separately. However, the two are inextricably related: as the cross-section preload increases, friction can prevent any motion in the longitudinal plane, and decreasing it can instead allow dangerous motions in the conductor ends. The latter can result in very high strains and, in Nb 3 Sn conductors, damage that can prevent the magnet to reach the desired performances. In an attempt to define design guidelines, in this paper we use simplified numerical models to compute, as a function of the in-plane prestress, the variation of the peak strains in the end region of the coils. Finally, we investigate the impact of the azimuthal prestress on a real magnet case, the High-Luminosity Nb 3 Sn Quadrupole MQXF.

Nb3Sn↗

Lattice Optimization for Porous Electrode

This code performs an optimization over the structure of a porous electrode formed from a lattice of unit cells. This is a steepest descent version of the code used in: V. A. Beck, J. J. Wong, C. F. Jekel, D. A. Tortorelli, S. E. Baker, E. B. Duoss and M. A. Worsley, Computational design of microarchitected porous electrodes for redox flow batteries, J. Power Sources, 2021, 512, 230453.

Wong, JonathanJ↗

SpectraCodec: A Hilbert curve-based method for encoding metadata in mass spectra for machine learning applications (SpectraCodec) v1

Machine learning approaches to mass spectrometry (MS) data analysis require structured metadata for optimal performance. However, current MS file formats necessitate external metadata sources, creating integration challenges that impede analytical workflows. Here, we present a novel approach for encoding metadata directly within mzML files using one-hot encoding of ASCII characters mapped via Hilbert space-filling curves. This strategy embeds metadata in the first spectrum's m/z-intensity space, ensuring persistence with the primary data, eliminating the need for external metadata files, and maintaining compatibility with existing MS software. We demonstrate that the Hilbert curve mapping efficiently utilizes the two-dimensional spectral space while maintaining robust data recovery. This method offers a practical solution for machine learning applications in mass spectrometry by ensuring metadata and spectral data remain unified through all stages of analysis.

Bowen, Benjamin [Lawrence Berkeley National Labora↗