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arXiv 2021年

作者： Takahashi, Shota Fukuda, Mituhiro Tanaka, Mirai Department of Statistical Science The Graduate University for Advanced Studies 10–3 Midori-cho Tachikawa Tokyo190–8562 Japan Department of Computer Science Institute of Mathematics and Statistics University of São Paulo Cidade Universitária Rua do Matão 1010 São Paulo05508–090 Brazil Department of Mathematical and Computing Science Tokyo Institute of Technology 2–12–1 Oh-okayama Meguro-ku Tokyo152–8552 Japan São Paulo State Technological College Praia Grande Praça 19 de Janeiro 144 SP Praia Grande11700–100 Brazil Department of Statistical Inference and Mathematics The Institute of Statistical Mathematics 10–3 Midori-cho Tachikawa Tokyo190–8562 Japan Continuous Optimization Team RIKEN Center for Advanced Intelligence Project Nihonbashi 1–chome Mitsui Building 15th floor 1–4–1 Nihonbashi Chuo-ku Tokyo103–0027 Japan

Difference of Convex (DC) optimization problems have objective functions that are differences between two convex functions. Representative ways of solving these problems are the proximal DC algorithms, which require that the convex part of the objective function have Lsmoothness. In this article, we propose the Bregman Proximal DC Algorithm (BPDCA) for solving large-scale DC optimization problems that do not possess L-smoothness. Instead, it requires that the convex part of the objective function has the L-smooth adaptable property that is exploited in Bregman proximal gradient algorithms. In addition, we propose an accelerated version, the Bregman Proximal DC Algorithm with extrapolation (BPDCAe), with a new restart scheme. We show the global convergence of the iterates generated by BPDCA(e) to a limiting critical point under the assumption of the Kurdyka-Lojasiewicz property or subanalyticity of the objective function and other weaker conditions than those of the existing methods. We applied our algorithms to phase retrieval, which can be described both as a nonconvex optimization problem and as a DC optimization problem. Numerical experiments showed that BPDCAe outperformed existing Bregman proximal-type algorithms because the DC formulation allows for larger admissible step *** Codes 90C26, 90C30, 65K05 Copyright © 2021, The Authors. All rights reserved.

关键词： Convex optimization

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THz Generation Control in Fe/X Spintronic Multilayers by chemical bonding at epitaxial Fe/GaAs(001) interfaces

THz Generation Control in Fe/X Spintronic Multilayers by che...

引用

Conference on Lasers and Electro-Optics (CLEO)

作者： Roman Adam Genyu Chen Daniel E. Bürgler Derang Cao Sarah Heidtfeld Debamitra Chakraborty Jing Cheng Ivan Komissarov Hilde Hardtdegen Martin Mikulics Claus M. Schneider Roman Sobolewski Research Centre Jülich Peter Grünberg Institute (PGI-6) Jülich Germany Materials Science Graduate Program University of Rochester Rochester New York USA Laboratory for Laser Energetics University of Rochester Rochester New York USA College of Physics Center for Marine Observation and Communications Qingdao University Qingdao China Department of Electrical and Computer Engineering University of Rochester Rochester New York USA Research Centre Jülich Ernst Ruska Centre for Microscopy and Spectroscopy with Electrons Jülich Germany Department of Physics University of California Davis Davis California USA

We report an additional degree of control of THz transients in Fe/X spintronic emitters grown on GaAs(001). We ascribe the field-independent enhancement of the THz amplitude to specific chemical bonding at the epitaxi... 详细信息

ISBN: (纸本)9781943580910

关键词： Electromagnetic radiation Free electron lasers Gallium arsenide Magnetic fields Terahertz generation Ultrafast lasers

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Revised JNLPBA corpus: A revised version of biomedical NER corpus for relation extraction task

arXiv

引用

arXiv 2019年

作者： Huang, Ming-Siang Lai, Po-Ting Tsai, Richard Tzong-Han Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang Ming University Taipei Taiwan Department of Computer Science National Tsing-Hua University Hsinchu Taiwan Intelligent Agent Systems Laboratory Institute of Information Science Academia Sinica Taipei Taiwan Intelligent Information Service Research Laboratory Department of Computer Science and Information Engineering National Central University Taoyuan Taiwan

The advancement of biomedical named entity recognition (BNER) and biomedical relation extraction (BRE) researches promotes the development of text mining in biological domains. As a cornerstone of BRE, robust BNER system is required to identify the mentioned NEs in plain texts for further relation extraction stage. However, the current BNER corpora, which play important roles in these tasks, paid less attention to achieve the criteria for BRE task. In this study, we present Revised JNLPBA corpus, the revision of JNLPBA corpus, to broaden the applicability of a NER corpus from BNER to BRE task. We preserve the original entity types including protein, DNA, RNA, cell line and cell type while all the abstracts in JNLPBA corpus are manually curated by domain experts again basis on the new annotation guideline focusing on the specific NEs instead of general terms. Simultaneously, several imperfection issues in JNLPBA are pointed out and made up in the new corpus. To compare the adaptability of different NER systems in Revised JNLPBA and JNLPBA corpora, the F1-measure was measured in three open sources NER systems including BANNER, Gimli and NERSuite. In the same circumstance, all the systems perform average 10% better in Revised JNLPBA than in JNLPBA. Moreover, the cross-validation test is carried out which we train the NER systems on JNLPBA/Revised JNLPBA corpora and access the performance in both protein-protein interaction extraction (PPIE) and biomedical event extraction (BEE) corpora to confirm that the newly refined Revised JNLPBA is a competent NER corpus in biomedical relation application. The revised JNLPBA corpus is freely available at ***/BNER/Content/Revised_***. Copyright © 2019, The Authors. All rights reserved.

关键词： Proteins

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Influence of Magnetic Fields on Electrochemical Reactions of Redox Cofactor Solutions

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Angewandte Chemie 2021年第33期133卷

作者： Jimin Park Florian Koehler Georgios Varnavides Marc-Joseph Antonini Prof. Dr. Polina Anikeeva Department of Materials Science and Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA Research Laboratory of Electronics and McGovern Institute for Brain Research Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA Harvard/MIT Health Science & Technology Graduate Program Cambridge MA 02139 USA Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA

Redox cofactors mediate many enzymatic processes and are increasingly employed in biomedical and energy applications. Exploring the influence of external magnetic fields on redox cofactor chemistry can enhance our understanding of magnetic-field-sensitive biological processes and allow the application of magnetic fields to modulate redox reactions involving cofactors. Through a combination of experiments and modeling, we investigate the influence of magnetic fields on electrochemical reactions in redox cofactor solutions. By employing flavin mononucleotide (FMN) cofactor as a model system, we characterize magnetically induced changes in Faradaic currents. We find that radical pair intermediates have negligible influence on current increases in FMN solution upon application of a magnetic field. The dominant mechanism underlying the observed current increases is the magneto-hydrodynamic effect. We extend our analyses to other diffusion-limited electrochemical reactions of redox cofactor solutions and arrive at similar conclusions, highlighting the opportunity to use this framework in redox cofactor chemistry.

关键词： electrochemistry magnetic field effects magneto-hydrodynamic effect radicals redox cofactors

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494P Evaluation of transcriptome forward computational strategies to improve molecular diagnosis in rare pediatric neuromuscular disease

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Neuromuscular Disorders 2024年 43卷 104441.331-104441.331页

作者： Silverstein, S. Ganapathy, K. Donkervoort, S. Moy, J. Uapinyoying, B. Gorokhova, S. Ganesh, V. Weisburd, B. Orbach, R. Foley, A. Mohammadi, P. Adams, D. Bonnemann, C. Neuromuscular and Neurogenetics Disorders of Childhood Section NINDS NIH Bethesda USA Undiagnosed Diseases Program NIH Bethesda USA Rutgers New Jersey Medical School Newark USA Department of Integrative Structural and Computational Biology Scripps Research Institute La Jolla USA Graduate College of Computing and Data Science Boston University Boston USA Center for Genetic Medicine Research Children's Research Institute Children's National Hospital Washington DC USA Aix Marseille Univ INSERM MMG Marseille France Department of Medical Genetics Timone Children's Hospital Marseille France The Broad Institute of MIT and Harvard Boston USA Center for Immunity and Immunotherapies Seattle Children's Research Institute Seattle USA Department of Pediatrics University of Washington School of Medicine Seattle USA Department of Genome Sciences University of Washington Seattle USA

Pediatric neuromuscular diseases are a genetically and clinically heterogenous group of disorders of which 30-60% remain molecularly undiagnosed even after evaluation with exome or genome sequencing. Estimates for added diagnostic benefit of transcriptomic sequencing range between 7-32% across different disease groups. Recently, open-source computational tools designed to systematically survey transcriptomic sequencing data for aberrant events have become available. In this study we assess the sensitivity of DROP (OUTRIDER, FRASER and MAE), MINTIE, LeafcutterMD, and ANEVA-H to detect known outliers in pediatric neuromuscular cohorts in order to identify the optimal set of tools for diagnostic use. Each tool selected utilizes a different statistical strategy and experimental design geared for rare disease. Tools were run on three transcriptome cohorts from the NINDS Neuromuscular and Neurogenetic Diseases of Childhood Section: muscle tissue (n=71), cycloheximide treated fibroblasts (n=79) and untreated fibroblasts (n=37). For splicing tools, MINTIE is the best performing tool (recall rate = 9/21, 42%), followed by FRASER (recall rate = 16/41, 36%), then LeafcutterMD (recall rate = 0/41, 0%). For expression outliers, OUTRIDER detects 6% of true positives (1/15), while the addition of healthy GTEx controls does not improve detection. For monoallelic expression, MAE and ANEVA-H will be compared. Additional evaluations to identify the optimal RNA library preparation methodology for these tools is also in progress. Thus far, OUTRIDER yielded one new candidate diagnosis of TRIP4 related disease. Analysis for new candidate variants is ongoing. Based on these results, and those of ongoing experiments, we will provide recommendations for the use of these tools in diagnostic pipelines for rare pediatric neuromuscular disease.

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The bulk van der Waals layered magnet CrSBr is a quasi-1D material

arXiv

引用

arXiv 2022年

作者： Klein, Julian Pingault, Benjamin Florian, Matthias Heißenbüttel, Marie-Christin Steinhoff, Alexander Song, Zhigang Torres, Kierstin Dirnberger, Florian Curtis, Jonathan B. Weile, Mads Penn, Aubrey Deilmann, Thorsten Dana, Rami Bushati, Rezlind Quan, Jiamin Luxa, Jan Sofer, Zdenek Alù, Andrea Menon, Vinod M. Wurstbauer, Ursula Rohlfing, Michael Narang, Prineha Lončar, Marko Ross, Frances M. Department of Materials Science and Engineering Massachusetts Institute of Technology CambridgeMA02139 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02138 United States QuTech Delft University of Technology Delft2600 GA Netherlands Department of Electrical and Computer Engineering Department of Physics University of Michigan Ann ArborMI48109 United States Institut für Festkörpertheorie Westfälische Wilhelms-Universität Münster Münster48149 Germany Institut für Theoretische Physik Universität Bremen P.O. Box 330 440 Bremen28334 Germany Bremen Center for Computational Materials Science University of Bremen Bremen28359 Germany Department of Physics City College of New York New YorkNY10031 United States College of Letters and Science UCLA Los AngelesCA90095 United States Department of Physics Technical University of Denmark Kgs. LyngbyDK-2800 Denmark MIT.nano Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics The Graduate Center City University of New York New YorkNY10016 United States Photonics Initiative CUNY Advanced Science Research Center New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States Department of Inorganic Chemistry University of Chemistry and Technology Prague Technická 5 Prague 6166 28 Czech Republic Institute of Physics Center for Nanotechnology University of Münster Münster48149 Germany

Correlated quantum phenomena in one-dimensional (1D) systems that exhibit competing electronic and magnetic order are of strong interest for studying fundamental interactions and excitations, such as Tomonaga-Luttinger liquids and topological orders and defects with properties completely different from the quasiparticles expected in their higher-dimensional counterparts. However, clean 1D electronic systems are difficult to realize experimentally, particularly magnetically ordered systems. Here, we show that the van der Waals layered magnetic semiconductor CrSBr behaves like a quasi-1D material embedded in a magnetically ordered environment. The strong 1D electronic character originates from the Cr-S chains and the combination of weak interlayer hybridization and anisotropy in effective mass and dielectric screening with an effective electron mass ratio of meX/meY ∼ 50. This extreme anisotropy experimentally manifests in strong electron-phonon and exciton-phonon interactions, a Peierls-like structural instability and a Fano resonance from a van Hove singularity of similar strength of metallic carbon nanotubes. Moreover, due to the reduced dimensionality and interlayer coupling, CrSBr hosts spectrally narrow (1 meV) excitons of high binding energy and oscillator strength that inherit the 1D character. Overall, CrSBr is best understood as a stack of weakly hybridized monolayers and appears to be an experimentally attractive candidate for the study of exotic exciton and 1D correlated many-body physics in the presence of magnetic order. Copyright © 2022, The Authors. All rights reserved.

关键词： Excitons

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Electron Acceleration in Carbon Nanotubes

arXiv

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arXiv 2025年

作者： Bonţoiu, Cristian Bonatto, Alexandre Apsimon, Öznur Bandiera, Laura Cavoto, Gianluca Drebot, Illya Gatti, Giancarlo Giner-Navarro, Jorge Lei, Bifeng Martín-Luna, Pablo Rago, Ilaria Pérez, Juan Rodríguez Nunes, Bruno Silveira Sytov, Alexei Valagiannopoulos, Costas Welsch, Carsten P. Xia, Guoxing Resta-López, Javier Department of Physics University of Liverpool Oxford Street LiverpoolL69 7ZE United Kingdom Graduate Program in Information Technology and Healthcare Management the Beam Physics Group Federal University of Health Sciences of Porto Alegre RS Porto Alegre90050-170 Brazil Department of Physics and Astronomy University of Manchester Oxford Road ManchesterM13 9PL United Kingdom Cockroft Institute Keckwick Lane Daresbury WarringtonWA4 4AD United Kingdom INFN Sezione di Ferrara Via Saragat 1 Ferrara44122 Italy Dipartimento di Fisica Sapienza Università di Roma Piazzale Aldo Moro 2 Roma00185 Italy INFN Sezione di Roma Piazzale Aldo Moro 2 Rome00185 Italy INFN Sezione di Milano Via G. Celoria 16 Milano20133 Italy Centro de Láseres Pulsados Building M5 Science Park Calle Adaja 8 Salamanca Villamayor37185 Spain Universidad de Valencia Paterna46071 Spain Universidad de Valencia CSIC Paterna46980 Spain Nuclear and Energy Research Institute IPEN–CNEN SP São Paulo Brazil National Technical University of Athens School of Electrical and Computer Engineering Zografou157 73 Greece Departamento de Física Aplicada y Electromagnetismo Universidad de Valencia Burjassot46100 Spain

Laser wakefield acceleration (LWFA) may achieve TeV/m gradients using high-density solid-state plasmas as accelerating media. However, the application of bulk solid materials requires attosecond laser pulses, such as X-ray lasers, to drive wakefields at these high densities. Additionally, the short wakefield wavelengths associated with solid-state plasmas greatly limit the accelerating length. An alternative approach employs 2D carbon-based nanomaterials, like graphene or carbon nanotubes (CNTs), configured into structured targets. These nanostructures are designed with voids or low-density regions to effectively reduce the overall plasma density. This reduction enables the use of longer-wavelength lasers and also extends the plasma wavelength and the acceleration length. In this study, we present, to our knowledge, the first numerical demonstration of electron acceleration via self-injection into a wakefield bubble driven by an infrared laser pulse in structured CNT targets, similar to the behavior observed in gaseous plasmas for LWFA in the nonlinear (or bubble) regime. Using the PIConGPU code, bundles of CNTs are modeled in a 3D geometry as 25 nm-thick carbon tubes with an initial density of 1022 cm−3. The carbon plasma is ionized by a three-cycle, 800 nm wavelength laser pulse with a peak intensity of 1021 W cm−2, achieving an effective plasma density of 1020 cm−3. The same laser also drives the wakefield bubble, responsible for the electron self-injection and acceleration. Simulation results indicate that fs-long electron bunches with hundreds of pC charge can be self-injected and accelerated at gradients exceeding 1 TeV/m. Both charge and accelerating gradient figures are unprecedented when compared with LWFA in gaseous plasma. © 2025, CC BY-NC-ND.

关键词： X ray lasers

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Diffusion and Security Evaluation of Feistel-PG

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Chinese Journal of Electronics 2017年第4期26卷 734-739页

作者： WANG Yanfeng WU Wenling ZHANG Lei Trusted Computing and Information Assurance Laboratory Institute of Software Graduate University of Chinese Academy of Sciences State Key Laboratory of Computer Science Institute of Software

Feistel-PG structure is a new specific Generalized Feistel structure(GFS) adopted in DBlock and LHash. Its main feature is adding a sbox-size permutation before the round function. Different choices of the permutation may affect the security property of ciphers with Feistel-PG structure but how it effects is not clear. We evaluate the values of diffusion round for all possible parameters and summarize the characteristics of optimum shuffles. The results show that one special kind of FeistelPG achieves full diffusion in less cost than the improved GFS. This advantage may attract the designers’ interests and this kind of Feistel-PG ciphers are suggested to designers. We also evaluate the security of suggested ciphers against various byte-oriented attacks, including differential cryptanalysis, linear cryptanalysis, impossible differential attack and integral attack. Some permutations with optimum diffusion but relatively weaker security are filtered out and these permutations should be avoided by designers.

关键词： Block cipher Diffusion Cryptanalysis GFS Feistel-PG

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Will artificial intelligence supersede earth system and climate models?

arXiv

引用

arXiv 2021年

作者： Irrgang, Christopher Boers, Niklas Sonnewald, Maike Barnes, Elizabeth A. Kadow, Christopher Staneva, Joanna Saynisch-Wagner, Jan Helmholtz Centre Potsdam German Research Centre for Geosciences GFZ Potsdam Germany Department of Mathematics and Computer Science Free University of Berlin Germany Potsdam Institute for Climate Impact Research Potsdam Germany Department of Mathematics and Global Systems Institute University of Exeter United Kingdom Program in Atmospheric and Oceanic Sciences Princeton University PrincetonNJ08540 United States NOAA OAR Geophysical Fluid Dynamics Laboratory Ocean and Cryosphere Division PrincetonNJ08540 United States University of Washington School of Oceanography SeattleWA United States Colorado State University Fort Collins United States German Climate Computing Center DKRZ Hamburg Germany Helmholtz-Zentrum Geesthacht Center for Material and Coastal Research HZG Geesthacht Germany

We outline a perspective of an entirely new research branch in Earth and climate sciences, where deep neural networks and Earth system models are dismantled as individual methodological approaches and reassembled as learning, self-validating, and interpretable Earth system model-network hybrids. Following this path, we coin the term"Neural Earth System Modelling" (NESYM) and highlight the necessity of a transdisciplinary discussion platform, bringing together Earth and climate scientists, big data analysts, and AI experts. We examine the concurrent potential and pitfalls of Neural Earth System Modelling and discuss the open question whether artificial intelligence will not only infuse Earth system modelling, but ultimately render them obsolete. © 2021, CC BY.

关键词： Climate models

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THz generation by exchange-coupled spintronic emitters

npj Spintronics

引用

npj Spintronics 2024年第1期2卷 1-8页

作者： Roman Adam Derang Cao Daniel E. Bürgler Sarah Heidtfeld Fangzhou Wang Christian Greb Markus Büscher Claus M. Schneider Jing Cheng Debamitra Chakraborty Ivan Komissarov Roman Sobolewski Martin Mikulics Hilde Hardtdegen Peter Grünberg Institute Research Centre Jülich Jülich Germany College of Physics Qingdao University Qingdao China Faculty of Physics University Duisburg-Essen Duisburg Germany Institut für Laser- und Plasmaphysik Heinrich-Heine Universität Düsseldorf Düsseldorf Germany Materials Science Graduate Program University of Rochester Rochester NY USA Laboratory for Laser Energetics University of Rochester Rochester NY USA Department of Electrical and Computer Engineering University of Rochester Rochester NY USA Ernst Ruska Centre Research Centre Jülich Jülich Germany

The mechanism of THz generation in ferromagnet/metal (F/M) bilayers has been typically ascribed to the inverse spin Hall effect (ISHE). Here, we fabricated Pt/Fe/Cr/Fe/Pt multilayers containing two back-to-back spintronic THz emitters separated by a thin (tCr≤ 3nm) wedge-shaped Cr spacer. In such an arrangement, magnetization alignment of the two Fe films can be controlled by the interplay between Cr-mediated interlayer exchange coupling (IEC) and an external magnetic field. This in turn results in a strong variation of the THz amplitudeA, withA↑↓reaching up to 14 timesA↑↑(arrows indicate the relative alignment of the magnetization of the two magnetic layers). This observed functionality is ascribed to the interference of THz transients generated by two closely spaced THz emitters. Moreover, the magnetic field dependenceA(H) shows a strong asymmetry that points to an additional performance modulation of the THz emitter via IEC and multilayer design.

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