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High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials

ChemBioChem 2022年第17期23卷 e202200310页

作者： Solares, Maria J. Jonaid, G.M. Luqiu, William Y. Berry, Samantha Khadela, Janki Liang, Yanping Evans, Madison C. Pridham, Kevin J. Dearnaley, William J. Sheng, Zhi Kelly, Deborah F. Molecular Cellular and Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park 16802 PA United States Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park 16802 PA United States Department of Biomedical Engineering Pennsylvania State University University Park 16802 PA United States Center for Structural Oncology Pennsylvania State University University Park 16802 PA United States Department of Electrical and Computer Engineering Duke University Durham 27708 NC United States Fralin Biomedical Research Institute at VTC Virginia Tech Roanoke 24016 VA United States

Mutations in tumor suppressor genes, such as Tumor Protein 53 (TP53), are heavily implicated in aggressive cancers giving rise to gain- and loss-of-function phenotypes. While individual domains of the p53 protein have been studied extensively, structural information for full-length p53 remains incomplete. Functionalized microprocessor chips (microchips) with properties amenable to electron microscopy permitted us to visualize complete p53 assemblies for the first time. The new structures revealed p53 in an inactive dimeric state independent of DNA binding. Residues located at the protein-protein interface corresponded with modification sites in cancer-related hot spots. Changes in these regions may amplify the toxic effects of clinical mutations. Taken together, these results contribute advances in technology and imaging approaches to decode native protein models in different states of activation. © 2022 Wiley-VCH GmbH.

关键词： cancer electron microscopy microchips p53, molecular modeling

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Topological Surface State Evolution in Bi2Se3 via Surface Etching

arXiv

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arXiv 2024年

作者： Yue, Ziqin Huang, Jianwei Wang, Ruohan Li, Jia-Wan Rong, Hongtao Guo, Yucheng Wu, Han Zhang, Yichen Kono, Junichiro Zhou, Xingjiang Hou, Yusheng Wu, Ruqian Yi, Ming Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Guangdong Provincial Key Laboratory of Magnetoelectric Physics and Devices Center for Neutron Science and Technology School of Physics Sun Yat-Sen University Guangzhou510275 China Institute of Physics Chinese Academy of Sciences Beijing100190 China Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Department of Physics and Astronomy University of California Irvine IrvineCA92697 United States

Topological insulators are materials with an insulating bulk interior while maintaining gapless boundary states against back scattering. Bi2Se3 is a prototypical topological insulator with a Dirac-cone surface state around Γ. Here, we present a controlled methodology to gradually remove Se atoms from the surface Se-Bi-Se-Bi-Se quintuple layers, eventually forming bilayer-Bi on top of the quintuple bulk. Our method allows us to track the topological surface state and confirm its robustness throughout the surface modification. Importantly, we report a relocation of the topological Dirac cone in both real space and momentum space, as the top surface layer transitions from quintuple Se-Bi-Se-Bi-Se to bilayer-Bi. Additionally, charge transfer among different surface layers is identified. Our study provides a precise method to manipulate surface configurations, allowing for the fine-tuning of the topological surface states in Bi2Se3, which represents a significant advancement towards nano-engineering of topological states. Copyright © 2024, The Authors. All rights reserved.

关键词： Topological insulators

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A radiomics-boosted deep-learning model for COVID-19 and non-COVID-19 pneumonia classification using chest X-ray image

arXiv

引用

arXiv 2021年

作者： Hu, Zongsheng Yang, Zhenyu Lafata, Kyle J. Yin, Fang-Fang Wang, Chunhao Medical Physics Graduate Program Duke Kunshan University Jiangsu Kunshan215316 China Department of Radiation Oncology Duke University DurhamNC27710 United States Department of Radiology Duke University DurhamNC27710 United States Department of Electrical and Computer Engineering Duke University DurhamNC27710 United States

Purpose: To develop a deep-learning model that integrates radiomics analysis for enhanced performance of COVID-19 and Non-COVID-19 pneumonia detection using chest X-ray image. Methods: Based on a pre-trained VGG-16 architecture, the deep-learning design consisted of a 5-Dense layer neural network with varying sizes, while the last three convolutional layers were set as free parameters for training. In radiomics analysis, a 2D sliding kernel was implemented to map the impulse response of radiomic features throughout the entire X-ray image;thus, each feature is rendered as a 2D map in the same dimension as X-ray image. For comparison purpose, a pilot model was trained using X-ray image only. Subsequently, 2 radiomic feature maps (RFMs) were selected based on cross-correlation analysis in reference to the pilot model saliency map results. The radiomics-boosted model was then trained based on the same deep-learning design using X-ray image plus the selected RFMs as input. Both models were developed using 812 chest X-ray images with 262/288/262 COVID-19/Non-COVID-19 pneumonia/healthy cases, and 649/163 cases were assigned as training-validation/independent test sets. For each model, 50 versions were trained with random assignments of training/validation cases following 7:1 ratio in the training-validation set. Sensitivity, specificity, accuracy, and ROC curves together with Area-Under-the-Curve (AUC) were compared between the two models. Results: The performance of detecting COVID-19 vs Non-COVID-19 pneumonia in the pilot model using X-ray image only were:1) sensitivity 0.90±0.07 vs 0.78±0.09, 2) specificity 0.94±0.04 vs 0.94±0.04, 3) accuracy 0.93±0.03 vs 0.89±0.03, and 4) ROC AUC 0.96±0.02 vs 0.92±0.04. Entropy and Short-Run-Emphasize were selected based on their high correlations with pilot model saliency map results. In the radiomics-boosted model, the corresponding results demonstrated significant improvements (p © 2021, CC BY-NC-ND.

关键词： Impulse response

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Enhanced Superconducting Qubit Performance Through Ammonium Fluoride Etch

arXiv

引用

arXiv 2024年

作者： Kopas, Cameron J. Goronzy, Dominic P. Pham, Thang Torres Castanedo, Carlos G. Cheng, Matthew Cochrane, Rory Nast, Patrick Lachman, Ella Zhelev, Nikolay Z. Vallières, André Murthy, Akshay A. Oh, Jin-Su Zhou, Lin Kramer, Matthew J. Cansizoglu, Hilal Bedzyk, Michael J. Dravid, Vinayak P. Romanenko, Alexander Grassellino, Anna Mutus, Josh Y. Hersam, Mark C. Yadavalli, Kameshwar Rigetti Computing BerkeleyCA United States Department of Materials Science and Engineering Northwestern University EvanstonIL United States Center for Applied Physics and Superconducting Technologies Northwestern University EvanstonIL United States Department of Physics and Astronomy Northwestern University EvanstonIL United States Department of Physics University of Oregon EugeneOR United States Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Fermi National Accelerator Laboratory BataviaIL United States Ames Laboratory U.S. Department of Energy AmesIA United States Northwestern University EvanstonIL United States Department of Chemistry Northwestern University EvanstonIL United States Department of Electrical and Computer Engineering Northwestern University EvanstonIL United States

The performance of superconducting qubits is often limited by dissipation and two-level systems (TLS) losses. The dominant sources of these losses are believed to originate from amorphous materials and defects at interfaces and surfaces, likely as a result of fabrication processes or ambient exposure. Here, we explore a novel wet chemical surface treatment at the Josephson junction-substrate and the substrate-air interfaces by replacing a buffered oxide etch (BOE) cleaning process with one that uses hydrofluoric acid followed by aqueous ammonium fluoride. We show that the ammonium fluoride etch process results in a statistically significant improvement in median T1 by ∼ 22% (p = 0.002), and a reduction in the number of strongly-coupled TLS in the tunable frequency range. Microwave resonator measurements on samples treated with the ammonium fluoride etch prior to niobium deposition also show ∼ 33% lower TLS-induced loss tangent compared to the BOE treated samples. As the chemical treatment primarily modifies the Josephson junction-substrate interface and substrate-air interface, we perform targeted chemical and structural characterizations to examine materials’ differences at these interfaces and identify multiple microscopic changes that could contribute to decreased TLS. © 2024, CC BY-NC-ND.

关键词： Fluorine compounds

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Structural and performance comparison between SU-8 microfabricated and 3D-printed microneedle electrodes

引用

Journal of 3D Printing in Medicine 2020年第1期4卷 29-44页

作者： Soltanzadeh, Ramin Afsharipour, Elnaz Anssari, Neda Mansouri, Behzad Shafai, Cyrus Biomedical Graduate Studies Program University of Manitoba Winnipeg R3T 5V6 MB Canada Electrical and Computer Engineering Department University of Manitoba Winnipeg R3T 5V6 MB Canada Department of Internal Medicine (Neurology) University of Manitoba Winnipeg R3A 1R9 MB Canada

Aim: This study is aimed to compare the structure and performance of 3D-printed and microfabricated microneedle arrays (MNAs). Materials & methods: MNAs were produced using either stereolithography printing or were micro-fabricated using SU-8 polymer. The structure of both MNA types were tested and compared through scanning electron microscopy. MNA performance was also evaluated through electrical impedence spectroscopy and nerve conduction velocity testing. Results & conclusion: The 3D-printed MNAs were shown to have higher gain than microfabricated MNAs at high frequencies. However, the selectivity of the microfabricated MNAs is more than 3D-printed MNAs. Scanning electron microscopy image comparison also showed significant differences between the output of the 3D-printed MNAs and the microfabricated MNAs. It was understood that the microfabricated MNAs' geometries are closer to the primary design than the 3D-printed MNAs. © 2020 Future Medicine Ltd.

关键词： 3D printing microfabrication microneedle array performance difference strucutral difference

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Deep-Strong Coupling between Cavity Photons and Terahertz TO Phonons in PbTe

Deep-Strong Coupling between Cavity Photons and Terahertz TO...

引用

2023 Conference on Lasers and Electro-Optics, CLEO 2023

作者： Baydin, Andrey Manjappa, Manukumara Mishra, Sobhan Subhra Xu, Hongjing Tay, Fuyang Kim, Dasom Hernandez, Felix G.G. Rappl, Paulo H.O. Abramof, Eduardo Singh, Ranjan Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Smalley-Curl Institute Rice University HoustonTX77005 United States Instrumentation and Applied Physics Department Indian Institute of Science Bangalore560012 India Center for Disruptive Photonic Technologies The Photonics Institute Nanyang Technological University 639798 Singapore Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Instituto de Física Universidade de Sao Paulo SP Sao Paulo05508-090 Brazil Laboratorio Associado de Sensores e Materiais Instituto Nacional de Pesquisas Espaciais SP Sao Jose dos Campos12201-970 Brazil Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 637371 Singapore Department of Material Science and NanoEngineering Rice University HoustonTX77005 United States

We have investigated the resonant coupling of photons with TO phonons in lead telluride in small-mode-volume terahertz cavities, observing a giant vacuum Rabi splitting on the order of the bare cavity-phonon frequency... 详细信息

ISBN: (纸本)9781957171258

关键词： Photons

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Numerical solution and linear stability analysis of fractional nonlinear Schrödinger equation (2+1) dimensions based on Newton-Raphson method

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AIP Conference Proceedings 2024年第1期3082卷

作者： Harish A. Mardi Marwan Ramli Nasaruddin Nasaruddin Said Munzir Muhammad Ikhwan Mathematics Graduate Program Faculty of Mathematics and Natural Sciences Universitas Syiah Kuala Banda Aceh 23111 Indonesia. Department of Mathematics Faculty of Mathematics and Natural Sciences Universitas Syiah Kuala Banda Aceh 23111 Indonesia. Electrical and Computer Engineering Department Universitas Syiah Kuala Banda Aceh 23111 Indonesia.

The Fractional Nonlinear Schrödinger Equation (FNLS) is an equation that is generally used to describe the interaction of boson particles in the trap potential. This paper discusses the stability of the stationary solution of the FNLS (2+1) dimensional equation using the Newton-Raphson method as a method for determining the stationary solution. The stability of the stationary solution of the FNLS is determined by analyzing the distribution of real-part and imaginary-part of eigenvalues listed on the complex plane. The results obtained in this study are found that the solution to the 1-dimensional FNLS is a stable system. This solution is obtained by analyzing the distribution of eigenvalues in the complex plane, where in the solution to the 1-dimensional FNLS there are only imaginary-part eigenvalues without any real-part eigenvalues. Unlike the case with the solution of the 2-dimensional FNLS equation, the eigenvalues obtained have a real-part of eigenvalues. These eigenvalues represent that the solution to the 2-dimensional FNLS equation is an unstable system. It is an indicator that the soliton which is the solution of the FNLS equation for the 2-dimensional case will be damaged for a certain time.

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Observation of current-induced switching in non-collinear antiferromagnetic IrMn3 by differential voltage measurements

arXiv

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arXiv 2021年

作者： Arpaci, Sevdenur Lopez-Dominguez, Victor Shi, Jiacheng Sánchez-Tejerina, Luis Garesci, Francesca Wang, Chulin Yan, Xueting Sangwan, Vinod K. Grayson, Matthew Hersam, Mark C. Finocchio, Giovanni Amiri, Pedram Khalili Department of Electrical and Computer Engineering Northwestern University EvanstonIL60208 United States Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Department of Mathematical and Computer Sciences Physical Sciences and Earth Sciences University of Messina Messina98166 Italy Department of Engineering University of Messina Messina98166 Italy Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of Chemistry Northwestern University EvanstonIL60208 United States

There is accelerating interest in developing memory devices using antiferromagnetic (AFM) materials, motivated by the possibility for electrically controlling AFM order via spin-orbit torques, and its read-out via magnetoresistive effects. Recent studies have shown, however, that high current densities create non-magnetic contributions to resistive switching signals in AFM/heavy metal (AFM/HM) bilayers, complicating their interpretation. Here we introduce an experimental protocol to unambiguously distinguish current-induced magnetic and nonmagnetic switching signals in AFM/HM structures, and demonstrate it in IrMn3/Pt devices. A six-terminal double-cross device is constructed, with an IrMn3 pillar placed on one cross. The differential voltage is measured between the two crosses with and without IrMn3 after each switching attempt. For a wide range of current densities, reversible switching is observed only when write currents pass through the cross with the IrMn3 pillar, eliminating any possibility of non-magnetic switching artifacts. Micromagnetic simulations support our findings, indicating a complex domain-mediated switching process. © 2021, CC BY.

关键词： Binary alloys

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Development of a Selective Wet-Chemical Etchant for 3D Structuring of Silicon via Nonlinear Laser Lithography

arXiv

引用

arXiv 2023年

作者： Borra, Mona Zolfaghari Radfar, Behrad Nasser, Hisham Çolakoğlu, Tahir Tokel, Onur Turnalı, Ahmet Demirtaş, Merve Ustunel, Hande Toffoli, Daniele Ömer İlday, F. Turan, Raşit Pavlov, Ihor Bek, Alpan ODTÜ-GÜNAM Middle East Technical University Ankara06800 Turkey Ankara06800 Turkey Department of Electronics and Nanoengineering Aalto University Tietotie 3 EspooFI-02150 Finland Department of Physics Engineering Ankara University Ankara06100 Turkey Department of Physics Bilkent University Ankara06800 Turkey UNAM National Nanotechnology Research Center Institute of Materials Science and Nanotechnology Bilkent University Ankara06800 Turkey Department of Electrical and Electronics Engineering Bilkent University Ankara06800 Turkey Department of Electrical and Computer Engineering Boston University 8 Saint Mary’s Street BostonMA02215 United States Ankara06800 Turkey Network Technologies Department TUBITAK ULAKBIM Ankara06800 Turkey Department of Chemical and Pharmaceutical Sciences Trieste University Trieste Italy IOM-CNR Istituto Officina dei Materiali Trieste34149 Italy Micro and Nanotechnology Graduate Program of Natural and Applied Sciences Middle East Technical Turkey

Recently-demonstrated high-quality three-dimensional (3D) subsurface laser processing inside crystalline silicon (c-Si) wafers opens a door to a wide range of novel applications in multidisciplinary research areas. Using this technique, a novel maskless micro-pillars with precise control on the surface reflection and coverage are successfully fabricated by etching the laser processed region of c-Si wafer. To achieve this, a particular selective wet chemical etching is developed to follow subsurface laser processing of c-Si to reveal the desired 3D structures with smooth surfaces. Here, we report the development of a novel chromium-free chemical etching recipe based on copper nitrate, which yields substantially smooth surfaces at high etch rate and selectivity on the both laser-processed Si surface and subsurface, i.e., without significant etching of the unmodified Si. Our results show that the etch rate and surface morphology are interrelated and strongly influenced by the composition of the adopted etching solution. After an extensive compositional study performed at room temperature, we identify an etchant with a selectivity of over 1600 times for laser-modified Si with respect to unmodified Si. We also support our findings using density functional theory calculations of HF and Cu adsorption energies, indicating significant diversity on the c-Si and laser-modified surfaces. Copyright © 2023, The Authors. All rights reserved.

关键词： Morphology

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Experimental Transmission of LTE Signal Using Visible Light Communications

Experimental Transmission of LTE Signal Using Visible Light ...

引用

SBMO/IEEE MTT-S International Conference on Microwave and Optoelectronics (IMOC)

作者： Marcelo de Oliveira Marco A. Fernandes Paulo Santos Fernando P. Guiomar Luis Nero Alves Alexandre A. P. Pohl Paulo P. Monteiro Graduate Program in Electrical and Computer Engineering (CPGEI) Federal University of Technology - Paranáa (UTFPR) Curitiba Brazil Instituto de Telecomunicações Aveiro Portugal University of Aveiro Portugal

ISBN: (数字)9781728130996

ISBN: (纸本)9781728131009

In this paper we present an implementation of a Long-Term Evolution (LTE) signal transmission using a visible light communications (VLC) setup. VLC is a novel technology that employs off-the-shelf LED lamps to offer high-speed wireless communication, specially at indoor environments, where reportedly the majority of wireless data traffic takes place. By using the optical wireless channel, we manage to transmit downlink LTE signals in distances of up to 3 m, while keeping an EVM lower than the limit compliant.

关键词： Long Term Evolution Visible light communication Wireless communication Optical receivers Light emitting diodes Optical transmitters Standards

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