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arXiv 2023年

作者： Maisuradze, Luka King, Megan C. Surovtsev, Ivan V. Mochrie, Simon G.J. Shattuck, Mark D. O’Hern, Corey S. Department of Molecular Biophysics and Biochemistry Yale University New HavenCT United States Department of Cell Biology Yale School of Medicine New HavenCT United States Department of Physics Yale University New HavenCT United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT United States

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix Aij, where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in Aij within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states. © 2023, CC BY.

关键词： Topology

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Dynamic Insights of Developing Functional Nanomaterials for Clean Energy and Microelectronics

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Yang, Judith C Hwang, Sooyeon Camino, Fernando Chemical and Petroleum Engineering Department University of Pittsburgh Pittsburgh PA United States Physics and Astronomy Department University of Pittsburgh Pittsburgh PA United States Center for Functional Nanomaterials Brookhaven National Lab Upton NY United States Materials Science and Engineering Program & Department of Mechanical Engineering State University of New York at Binghamton Binghamton NY United States

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Large spin Hall effect in Si at room temperature

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Physical Review B 2020年第9期101卷 094435-094435页

作者： Paul C. Lou Anand Katailiha Ravindra G. Bhardwaj Tonmoy Bhowmick W. P. Beyermann Roger K. Lake Sandeep Kumar Department of Mechanical Engineering University of California Riverside California 92521 USA Department of Electrical Engineering and Computer Science University of California Riverside California 92521 USA Department of Physics and Astronomy University of California Riverside California 92521 USA Materials Science and Engineering Program University of California Riverside California 92521 USA

Silicon's weak intrinsic spin-orbit coupling and centrosymmetric crystal structure are a critical bottleneck to the development of Si spintronics, because they lead to an insignificant spin Hall effect (spin current generation) and inverse spin Hall effect (spin current detection). Here, we undertake current, magnetic field, crystallography dependent magnetoresistance, and magnetothermal transport measurements to study the spin transport behavior in freestanding Si thin films. We observe a large spin Hall magnetoresistance in both p−Si and n−Si at room temperature and it is an order of magnitude larger than that of Pt. One explanation of the unexpectedly large and efficient spin Hall effect is spin-phonon coupling instead of spin-orbit coupling. The macroscopic origin of the spin-phonon coupling can be large strain gradients that can exist in the freestanding Si films. This discovery in a light, earth abundant and centrosymmetric material opens a new path of strain engineering to achieve spin dependent properties in technologically highly developed materials.

关键词： Spin Hall magnetoresistance Spintronics Doped semiconductors

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Hierarchically Porous C/Fe3C Membranes with Fast Ion-Transporting Channels and Polysulfide-Trapping Networks for High-Areal-Capacity Li-S Batteries

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Nano letters 2020年第1期20卷 701-708页

作者： Xiangcun Li Yue Zhang Shuting Wang Yang Liu Yu Ding Gaohong He Ning Zhang Guihua Yu State Key Laboratory of Fine Chemicals Chemical Engineering Department Dalian University of Technology Dalian 116024 China. Materials Science and Engineering Program and Department of Mechanical Engineering The University of Texas at Austin Austin Texas 78712 United States.

We report here highly scalable yet stackable C/FeC membranes with fast ion-transport micro-/nanochannels and polysulfide-trapping networks via a facile phase-inversion process for high-areal-capacity Li-S batteries. The membrane cathodes with aligned channels and hierarchically porous networks significantly promote Li and electron transportation and meanwhile trap soluble polysulfide intermediates (LiPSs) effectively via strong chemical adsorption of the doped FeC nanoparticles in the membrane toward LiPSs. We further demonstrated that five-layer membrane electrodes with high S loading of 7.1 mg cm were readily prepared via layer-by-layer stacking of the C/FeC membrane, which can deliver a high capacity of 726 mA h g after 100 cycles, corresponding to an ultra-high-areal-capacity of 5.15 mA h cm at a low electrolyte/sulfur (/) ratio of 6.4 μL mg. The scalable multifunctional membrane electrodes with excellent electrochemical performance under high-sulfur-loading and lean electrolyte conditions reveal its promising applications in practical Li-S batteries.

关键词： Li−S batteries ion channels phase inversion polysulfide trapping porous membrane

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Polarization-Tunable Colorimetric Metasurfaces for All-Optical and Non-Destructive Structural Characterization of Polymeric Nanofibers

arXiv

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arXiv 2025年

作者： Kirya, Paula Hochberg, Justin D. Kim, Han Sol Haddadin, Zaid Bordy, Samantha Byun, Jiuk Pokorski, Jonathan K. Poulikakos, Lisa V. Department of Mechanical and Aerospace Engineering UC San Diego La Jolla CA United States Aiiso Yufeng Li Family Department of Chemical and Nano Engineering UC San Diego La Jolla CA United States Department of Electrical and Computer Engineering UC San Diego La Jolla CA United States Program in Materials Science and Engineering UC San Diego La Jolla CA United States

Metasurfaces have pioneered significant improvements in sensing technology by tailoring strong optical responses to weak signals. When designed with anisotropic subwavelength geometries, metasurfaces can tune responses to varying polarization states of light. Leveraging this to quantify structural alignment in fibrous materials unveils an alternative to destructive characterization methods. This work introduces metasurface-enhanced polarized light microscopy (Meta-PoL), which employs polarization-tunable, guided-mode-resonant colorimetric metasurfaces to characterize molecular and bulk alignment of poly(Ε-caprolactone) (PCL) nanofibers in a far-field configuration. PCL nanofibers drawn at 0%, 400%, and 900% ratios were interfaced with the studied metasurfaces. Metasurface resonances coinciding with the intrinsic drawn nanofiber resonances – confirmed by Stokes Polarimetry – produced the strongest colorimetric enhancement, resultant from alignment-specific nanofiber reflectivity. The enhancement degree corresponded with molecular and bulk alignments for each draw ratio, as measured through differential scanning calorimetry and scanning electron microscopy, respectively. Thus, Meta-PoL presents an all-optical, non-destructive, and quantitative measurement of nanofiber alignment. Copyright © 2025, The Authors. All rights reserved.

关键词： Differential scanning calorimetry

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Diopside-based Bioactive Glass-Ceramic Nanoparticles for Osteoimmunomodulation

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Ceramics International 2025年

作者： Sun Latt Pedram Sotoudehbagha Valeria Cardenas Andres Larraza Mehdi Razavi Biionix (Bionic Materials Implants & Interfaces) Cluster Department of Medicine University of Central Florida College of Medicine Orlando FL 32827 USA Burnett School of Biomedical Sciences University of Central Florida College of Medicine Orlando FL 32827 USA Department of Materials Science and Engineering University of Central Florida Orlando FL 32816 USA Biomedical Engineering Program Department of Mechanical and Aerospace Engineering University of Central Florida Orlando Florida 32816 USA

The objective of this study was to develop and characterize an osteoimmunomodulatory diopside-based glass-ceramic nanoparticle synthesized using a sol-gel synthesis method. Hydroxyapatite nanoparticles were utilized as a gold standard control. X-ray diffraction, transmission electron microscopy, scanning electron microscopy equipped with energy dispersive spectroscopy, dynamic light scattering, and zeta-potential analysis were performed to characterize the crystalline phase, morphology, microstructure, composition, hydrodynamic size distribution, and surface charge, respectively. Weight loss, pH, and ion release were measured after immersion of glass-ceramic nanoparticles in simulated body fluid to evaluate the nanoparticle’s biodegradation, showing ranges of Ca 2+ , Mg 2+ , and Si 4+ ion release previously found to be osteogenic and angiogenic. Cytocompatibility with human bone-marrow-derived mesenchymal stem cells and murine RAW264.7 macrophages was studied using metabolic activity (MTT) and live/dead fluorescent assays, demonstrating dose-dependent cytotoxicity in RAW264.7 cells and excellent biocompatibility with mesenchymal stem cells. The effect of the nanoparticles on M1/M2 macrophage polarization potential was evaluated through ELISA and phase-contrast image analysis. Our glass-ceramic nanoparticle promoted greater M2-associated anti-inflammatory IL-1ra cytokine release than M1-associated pro-inflammatory TNF-α release compared to hydroxyapatite nanoparticles, though significant morphological changes were not observed. These results indicate that our glass-ceramic nanoparticle is a promising osteoimmunomodulatory biomaterial for bone regenerative applications.

关键词： Stem cells

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Modeling the Effect of Over-discharge Cycling on Li-ion Batteries

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Journal of The Electrochemical Society 2025年第5期172卷 050534-050534页

作者： Raghav Sai Thiagarajan Anthony Concepción Deepti Tewari Judith A. Jeevarajan Vinay Premnath Venkat R. Subramanian Materials Science and Engineering Program Texas Materials Institute The University of Texas at Austin Austin Texas 78712 United States of America Walker Department of Mechanical Engineering & Material Science Engineering Texas Materials Institute The University of Texas at Austin Austin Texas 78712 United States of America Electrochemical Safety Research Institute UL Research Institutes 5000 Gulf Fwy UHTB Houston Texas 77204 United States of America Affiliate Faculty Oden Institute for Computational Science and Engineering The University of Texas at Austin Austin Texas 78712 United States of America

Off-nominal circumstances inducing cell over-discharge in a battery are of concern due to electrolyte decomposition and prolonged degradation effects. Copper dissolution and its subsequent deposition could lead to high cell temperatures and, in some cases, catastrophic failures during the battery's operational lifetime. Extending physics-based lithium-ion battery models for the purpose of simulating over-discharge conditions require key considerations in model parameters, constitutive equations, and the state of charge window of operation. This paper reports a reduced-order model for over-discharge and simulating its effect under various scenarios using a thermal tanks-in-series (TTiS) approach. The model was used to compare voltage-time behavior and capacity fade during cycling for different over-discharge cycling protocols. The efficacy of cycling simulations was validated with experimental data, and the TTiS model demonstrates reasonable agreement with the voltage, temperature, and capacity fade trends under the given experimental cycling regimes.

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Single-Shot Compressed Photoacoustic Tomographic Imaging with a Single Detector in a Scattering Medium

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Physical Review Applied 2020年第4期13卷 044009-044009页

作者： Yuning Guo Baowen Li Xiaobo Yin Department of Mechanical Engineering University of Colorado Boulder Boulder Colorado 80309 USA Department of Physics University of Colorado Boulder Boulder Colorado 80309 USA Materials Science and Engineering Program University of Colorado Boulder Boulder Colorado 80309 USA

Photon scattering imposes a fundamental restriction on optical imaging in turbid media. In this work, we propose a compressive-sensing-based photoacoustic imaging modality that allows single-shot tomography with a single detector in a scattering medium. The nonuniform optical speckle grains created in the diffusive regime, which act as a conventional drawback of optical modality, are used to generate ultrasound locally. The photoacoustic signals from spatial positions can be well extracted from a superimposed signal via introduction of locally modulated time delays. Taking advantage of the compressed measurement assisted by the acoustic mask, we demonstrate a theoretical compressed framework of three-dimensional photoacoustic surface tomography with a broad field of view after one-time optical illumination. This approach can increase the photoacoustic imaging efficiency greatly and reveals the potential for dynamic imaging in optically diffusive media.

关键词： Acoustic interactions Acoustic modeling Tomography Ultrasonics Acoustic techniques Medical imaging Optical techniques

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Toughening mechanisms of the elytra of the diabolical ironclad beetle (vol 586, pg 543, 2020)

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NATURE 2021年第7844期590卷 E21-E21页

作者： Rivera, Jesus Hosseini, Maryam Sadat Restrepo, David Murata, Satoshi Vasile, Drago Parkinson, Dilworth Y. Barnard, Harold S. Arakaki, Atsushi Zavattieri, Pablo Kisailus, David Materials Science and Engineering Program University of California Riverside CA USA Department of Chemical and Environmental Engineering University of California Riverside CA USA Department of Materials Science and Engineering University of California Irvine CA USA Lyles School of Civil Engineering Purdue University West Lafayette IN USA Department of Mechanical Engineering The University of Texas at San Antonio San Antonio TX USA Institute of Global Innovation Research Tokyo University of Agriculture and Technology Koganei Tokyo Japan Advanced Light Source Lawrence Berkeley National Laboratory Berkeley CA USA

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Revealing the Solid-State Electrolyte Interfacial Stability Model with Na–K Liquid Alloy

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Angewandte Chemie 2022年第29期134卷

作者： Xuelin Guo Dr. Yijie Liu Xiao Zhang Zhengyu Ju Dr. Yutao Li Prof. Dr. David Mitlin Prof. Dr. Guihua Yu Materials Science and Engineering Program and Walker Department of Mechanical Engineering The University of Texas at Austin 204 E Dean Keeton Street Austin TX 78712 USA

In this work, the Na–K liquid alloy with a charge selective interfacial layer is developed to achieve an impressively long cycling life with small overpotential on a sodium super-ionic conductor solid-state electrolyte (NASICON SSE). With this unique multi-cation system as the platform, we further propose a unique model that contains a chemical decomposition domain and a kinetic decomposition domain for the interfacial stability model. Based on this model, two charge selection mechanisms are proposed with dynamic chemical kinetic equilibrium and electrochemical kinetics as the manners of control, respectively, and both are validated by the electrochemical measurements with microscopic and spectroscopic characterizations. This study provides an effective design for high-energy-density solid-state battery with alkali Na–K anode, but also presents a novel approach to understand the interfacial chemical processes that could inspire and guide future designs.

关键词： Alkali Metal Batteries Interfacial Chemistry Liquid Metal Anode Multi-Cation Anode Solid-State Electrolyte

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