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Imaging atomic-scale chemistry from fused multi-modal electron microscopy

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npj computational Materials 2022年第1期8卷 164-171页

作者： Jonathan Schwartz Zichao Wendy Di Yi Jiang Alyssa J.Fielitz Don-Hyung Ha Sanjaya D.Perera Ismail El Baggari Richard D.Robinson Jeffrey A.Fessler Colin Ophus Steve Rozeveld Robert Hovden Department of Materials Science and Engineering University of MichiganAnn ArborMIUSA Mathematics and Computer Science Division Argonne National LaboratoryLemontILUSA Advanced Photon Source Facility Argonne National LaboratoryLemontILUSA Dow Chemical Co. MidlandMIUSA Department of Material Science and Engineering Cornell UniversityIthacaNew YorkUSA School of Integrative Engineering Chung-Ang UniversitySeoulRepublic of Korea Department of Physics Cornell UniversityIthacaNYUSA The Rowland Institute at Harvard CambridgeMAUSA Department of Electrical Engineering and Computer Science University of MichiganAnn ArborMIUSA National Center for Electron Microscopy Lawrence Berkeley National LaboratoryMolecular FoundryBerkeleyCAUSA Applied Physics Program University of MIchiganAnn ArborMIUnited States

Efforts to map atomic-scale chemistry at low doses with minimal noise using electron microscopes are fundamentally limited by inelastic ***,fused multi-modal electron microscopy offers high signal-to-noise ratio(SNR)recovery of material chemistry at nano-and atomic-resolution by coupling correlated information encoded within both elastic scattering(high-angle annular dark-field(HAADF))and inelastic spectroscopic signals(electron energy loss(EELS)or energy-dispersive x-ray(EDX)).By linking these simultaneously acquired signals,or modalities,the chemical distribution within nanomaterials can be imaged at significantly lower doses with existing detector *** many cases,the dose requirements can be reduced by over one order of *** high SNR recovery of chemistry is tested against simulated and experimental atomic resolution data of heterogeneous nanomaterials.

关键词： materials chemistry fused

Chang’e 3 lunar mission and upper limit on stochastic background of gravitational wave around the 0.01 Hz band

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arXiv 2017年

作者： Tang, Wenlin Xu, Peng Hu, Songjie Cao, Jianfeng Dong, Peng Bu, Yanlong Chena, Lue Han, Songtao Gong, Xuefei Lie, Wenxiao Ping, Jinsong Lau, Yun-Kau Tang, Geshi Science and Technology on Aerospace Flight Dynamics Laboratory Beijing Aerospace Control Center Beijing China Institute of Applied Mathematics Morningside Center of Mathematics and LESC Institute of Computational Mathematics Academy of Mathematics and System Science Chinese Academy of Sciences Beijing China Department of Aerospace Guidance Navigation and Control School of Astronautics Beihang University Beijing China Beijing Institute of Aerospace Control Devices Beijing China National astronomical observatories Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China

The Doppler tracking data of the Chang’e 3 lunar mission is used to constrain the stochastic background of gravitational wave in cosmology within the 1 mHz to 0.05 Hz frequency band. Our result improves on the upper bound on the energy density of the stochastic background of gravitational wave in the 0.02 Hz to 0.05 Hz band obtained by the Apollo missions, with the improvement reaching almost one order of magnitude at around 0.05 Hz. Detailed noise analysis of the Doppler tracking data is also presented, with the prospect that these noise sources will be mitigated in future Chinese deep space missions. A feasibility study is also undertaken to understand the scientific capability of the Chang’e 4 mission, due to be launched in 2018, in relation to the stochastic gravitational wave background around 0.01 Hz. Copyright © 2017, The Authors. All rights reserved.

关键词： Stochastic systems

ABACUS: An Electronic Structure Analysis Package for the AI Era

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arXiv 2025年

作者： Zhou, Weiqing Zheng, Daye Liu, Qianrui Lu, Denghui Liu, Yu Lin, Peize Huang, Yike Peng, Xingliang Bao, Jie J. Cai, Chun Jin, Zuxin Wu, Jing Zhang, Haochong Jin, Gan Ji, Yuyang Shen, Zhenxiong Liu, Xiaohui Sun, Liang Cao, Yu Sun, Menglin Liu, Jianchuan Chen, Tao Liu, Renxi Li, Yuanbo Han, Haozhi Liang, Xinyuan Bao, Taoni Chen, Nuo Ren, Hongxu Zhang, Xiaoyang Liu, Zhaoqing Fu, Yiwei Liu, Maochang Li, Zhuoyuan Wen, Tongqi Tang, Zechen Xu, Yong Duan, Wenhui Wang, Xiaoyang Gu, Qiangqiang Dai, Fu-Zhi Zheng, Qijing Zhao, Jin Zhang, Yuzhi Ou, Qi Jiang, Hong Liu, Shi Xu, Ben Xu, Shenzhen Ren, Xinguo He, Lixin Zhang, Linfeng Chen, Mohan AI for Science Institute Beijing100080 China HEDPS CAPT School of Physics College of Engineering Peking University Beijing100871 China College of Engineering Peking University Beijing100871 China Institute of Artificial Intelligence Hefei Comprehensive National Science Center Hefei230026 China Key Laboratory of Quantum Information University of Science and Technology of China Hefei230026 China Supercomputing Center University of Science and Technology of China Anhui Hefei230026 China Institute of Physics Chinese Academy of Sciences Beijing100190 China School of Materials Science and Engineering Peking University Beijing100871 China School of Electrical Engineering and Electronic Information Xihua University Chengdu610039 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China College of Chemistry and Molecular Engineering Peking University Beijing100871 China International Research Center for Renewable Energy State Key Laboratory of Multiphase Flow Xi’an Jiaotong University Shaanxi Xi’an710049 China Suzhou Academy of Xi’an Jiaotong University Jiangsu Suzhou215123 China Center for Structural Materials Department of Mechanical Engineering The University of Hong Kong Hong Kong The University of Hong Kong Shenzhen China State Key Laboratory of Low Dimensional Quantum Physics Department of Physics Tsinghua University Beijing100084 China Frontier Science Center for Quantum Information Beijing China Saitama Wako351-0198 Japan Institute for Advanced Study Tsinghua University Beijing100084 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China School of Artificial Intelligence and Data Science University of Science and Technology of China Hefei230026 China School of Materials Science and Engineering University of Science and Technology Beijing Beijing100083 China Department of Physics University of Science and

ABACUS (Atomic-orbital Based Ab-initio Computation at USTC) is an open-source software for first-principles electronic structure calculations and molecular dynamics simulations. It mainly features density functional theory (DFT) and is compatible with both plane-wave basis sets and numerical atomic orbital basis sets. ABACUS serves as a platform that facilitates the integration of various electronic structure methods, such as Kohn-Sham DFT, stochastic DFT, orbital-free DFT, and real-time time-dependent DFT, etc. In addition, with the aid of high-performance computing, ABACUS is designed to perform efficiently and provide massive amounts of first-principles data for generating general-purpose machine learning potentials, such as DPA models. Furthermore, ABACUS serves as an electronic structure platform that interfaces with several AI-assisted algorithms and packages, such as DeePKS-kit, DeePMD, DP-GEN, DeepH, DeePTB, etc. Copyright © 2025, The Authors. All rights reserved.

关键词： Stochastic systems

OPERATORS ON ANTI-DUAL PAIRS: LEBESGUE DECOMPOSITION VIA ARLINSKII’S ITERATION

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arXiv 2024年

作者： Göde, Ábel Tarcsay, Zsigmond Department of Applied Analysis and Computational Mathematics Eötvös Loránd University Pázmány Péter sétány 1/c. BudapestH-1117 Hungary Department of Mathematics Corvinus University of Budapest IX. Fővám tér 13-15. BudapestH-1093 Hungary

The aim of this paper is to prove a general Lebesgue decomposition theorem for positive operators on so-called anti-dual pairs, following the iterative approach introduced by Arlinskii. This procedure and the resulting theorem encompass several special cases, including positive operators on Hilbert spaces, non-negative forms on vector spaces, and representable functionals over *-*** Codes 47B65, 47A07 Copyright © 2024, The Authors. All rights reserved.

关键词： Vector spaces

Benchmarking the Immersed Boundary Method for Viscoelastic Flows

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arXiv 2023年

作者： Gruninger, Cole Barrett, Aaron Fang, Fuhui Forest, M. Gregory Griffith, Boyce E. Department of Mathematics University North Carolina Chapel HillNC United States Department of Mathematics University of Utah Salt Lake CityUT United States Department of Applied Physical Sciences University of North Carolina Chapel HillNC United States Department of Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina School of Medicine Chapel HillNC United States McAllister Heart Institute University of North Carolina School of Medicine Chapel HillNC United States

We present and analyze a series of benchmark tests regarding the application of the immersed boundary (IB) method to viscoelastic flows through and around non-trivial, stationary geometries. The IB method is widely used for the simulation of biological fluid dynamics and other modeling scenarios where a structure is immersed in a fluid. Although the IB method has been most commonly used to model systems with viscous incompressible fluids, it also can be applied to visoelastic fluids, and has enabled the study of a wide variety of dynamical problems including the settling of vesicles and the swimming of elastic filaments in fluids modeled by the Oldroyd-B constuitive equation. However, to date, relatively little work has explored the accuracy or convergence properties of the numerical scheme. Herein, we present benchmarking results for an IB solver applied to viscoelastic flows in and around non-trivial geometries using the idealized Oldroyd-B and more realistic, polymer-entanglement-based Rolie-Poly constitutive equations. We use two-dimensional numerical test cases along with results from rheology experiments to benchmark the IB method and compare it to more complex finite element and finite volume viscoelastic flow solvers. Additionally, we analyze different choices of regularized delta function and relative Lagrangian grid spacings which allow us to identify and recommend the key choices of these numerical parameters depending on the present flow regime. Copyright © 2023, The Authors. All rights reserved.

关键词： Benchmarking

Interacting models for twisted bilayer graphene: a quantum chemistry approach

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arXiv 2022年

作者： Faulstich, Fabian M. Stubbs, Kevin D. Zhu, Qinyi Soejima, Tomohiro Dilip, Rohit Zhai, Huanchen Kim, Raehyun Zaletel, Michael P. Chan, Garnet Kin-Lic Lin, Lin Department of Mathematics University of California BerkeleyCA94720 United States Department of Physics University of California BerkeleyCA94720 United States Division of Chemistry and Chemical Engineering California Institute of Technology PasadenaCA91125 United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

The nature of correlated states in twisted bilayer graphene (TBG) at the magic angle has received intense attention in recent years. We present a numerical study of an interacting Bistritzer-MacDonald (IBM) model of TBG using a suite of methods in quantum chemistry, including Hartree-Fock, coupled cluster singles, doubles (CCSD), and perturbative triples (CCSD(T)), as well as a quantum chemistry formulation of the density matrix renormalization group method (DMRG). Our treatment of TBG is agnostic to gauge choices, and hence we present a new gauge-invariant formulation to detect the spontaneous symmetry breaking in interacting models. To benchmark our approach, we focus on a simplified spinless, valleyless IBM model. At integer filling (ν = 0), all numerical methods agree in terms of energy and C2zT symmetry breaking. Additionally, as part of our benchmarking, we explore the impact of different schemes for removing "double-counting" in the IBM model. Our results at integer filling suggest that cross-validation of different IBM models may be needed for future studies of the TBG system. After benchmarking our approach at integer filling, we perform the first systematic study of the IBM model near integer filling (for |ν| Copyright © 2022, The Authors. All rights reserved.

关键词： Quantum chemistry

Alignment of density maps in Wasserstein distance

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Biological imaging 2024年 4卷 e5页

作者： Amit Singer Ruiyi Yang Department of Mathematics Princeton University Princeton NJ USA. Program in Applied and Computational Mathematics Princeton University Princeton NJ USA.

In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function enjoys a more benign landscape than its Euclidean counterpart and Bayesian optimization is employed for computation. Numerical experiments show improved accuracy and efficiency over existing algorithms on the alignment of real protein molecules. In the context of aligning heterogeneous pairs, we illustrate a potential need for new distance functions.

关键词： Bayesian optimization Wasserstein distance cryogenic electron microscopy heterogeneity analysis volume alignment

The ESPRIT algorithm under high noise: Optimal error scaling and noisy super-resolution

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arXiv 2024年

作者： Ding, Zhiyan Epperly, Ethan N. Lin, Lin Zhang, Ruizhe Department of Mathematics University of California Berkeley United States Department of Computing and Mathematical Sciences California Institute of Technology PasadenaCA United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory United States Challenge Institute for Quantum Computation University of California Berkeley United States Simons Institute for the Theory of Computing United States

Subspace-based signal processing techniques, such as the Estimation of Signal Parameters via Rotational Invariant Techniques (ESPRIT) algorithm, are popular methods for spectral estimation. These algorithms can achieve the so-called super-resolution scaling under low noise conditions, surpassing the well-known Nyquist limit. However, the performance of these algorithms under high-noise conditions is not as well understood. Existing state-of-the-art analysis indicates that ESPRIT and related algorithms can be resilient even for signals where each observation is corrupted by statistically independent, mean-zero noise of size O(1), but these analyses only show that the error ∊ decays at a slow rate ∊ = O͂(n−1/2) with respect to the cutoff frequency n (i.e., the maximum frequency of the measurements). In this work, we prove that under certain assumptions, the ESPRIT algorithm can attain a significantly improved error scaling ∊ = O͂(n−3/2), exhibiting noisy super-resolution scaling beyond the Nyquist limit ∊ = O(n−1) given by the Nyquist-–Shannon sampling theorem. We further establish a theoretical lower bound and show that this scaling is optimal. Our analysis introduces novel matrix perturbation results, which could be of independent interest. © 2024, CC BY.

关键词： Cutoff frequency

Setting the physical scale of dimensional reduction in causal dynamical triangulations

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Physical Review D 2019年第2期100卷 026014-026014页

作者： Joshua H. Cooperman Manuchehr Dorghabekov Department of Physics and Astronomy Bucknell University Lewisburg Pennsylvania 17837 USA Physics Program Bard College Annandale-on-Hudson New York 12504 USA* Applied Mathematics and Informatics Program American University of Central Asia Bishkek Kyrgyz Republic*

Within the causal dynamical triangulations approach to the quantization of gravity, striking evidence has emerged for the dynamical reduction of spacetime dimension on sufficiently small scales. Specifically, the spectral dimension decreases from the topological value of 4 toward a value near 2 as the scale being probed decreases. The physical scales over which this dimensional reduction occurs have not previously been ascertained. We present and implement a method to determine these scales in units of either the Planck length or the quantum spacetime geometry’s effective de Sitter length. We find that dynamical reduction of the spectral dimension occurs over physical scales of the order of 10 Planck lengths, which, for the numerical simulation considered below, corresponds to the order of 10−1 de Sitter lengths.

关键词： Quantum gravity