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Proceedings of the 31st International Conference on Neural Information Processing Systems

作者： Emmanuel Abbe Sanjeev Kulkarni Eun Jee Lee Program in Applied and Computational Mathematics and The Department of Electrical Engineering Princeton University The Department of Electrical Engineering Princeton University Program in Applied and Computational Mathematics

ISBN: (纸本)9781510860964

This paper develops upper and lower bounds on the influence measure in a network, more precisely, the expected number of nodes that a seed set can influence in the independent cascade model. In particular, our bounds exploit nonbacktracking walks, Fortuin-Kasteleyn-Ginibre type inequalities, and are computed by message passing algorithms. Nonbacktracking walks have recently allowed for headways in community detection, and this paper shows that their use can also impact the influence computation. Further, we provide parameterized versions of the bounds that control the trade-off between the efficiency and the accuracy. Finally, the tightness of the bounds is illustrated with simulations on various network models.

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Ab Initio Study of Single-and Double-Electron Capture Processes in Collisions of He^(2+) Ions and Ne Atoms

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Chinese physics Letters 2021年第11期38卷 30-36页

作者： Xiao-Xia Wang Kun Wang Yi-Geng Peng Chun-Hua Liu Ling Liu Yong Wu Heinz-Peter Liebermann Robert JBuenker Yi-Zhi Qu College of Material Sciences and Optoelectronic Technology University of Chinese Academy of SciencesBeijing 100049China Institute of Environmental Science Shanxi UniversityTaiyuan 030006China Department of Applied Physics Nanjing University of Science and TechnologyNanjing 210094China School of Physics Southeast UniversityNanjing 210094China Data Center for High Energy Density Physics Institute of Applied Physics and Computational MathematicsBeijing 100088China Fachbereich C-Mathematik und Naturwissenschaften Bergische Universitat WuppertalD-42097 WuppertalGermany

The single-and double-electron capture(SEC, DEC) processes of He^(2+) ions colliding with Ne atoms are studied by utilizing the full quantum-mechanical molecular-orbital close-coupling method. Total and state-selective SEC and DEC cross sections are presented in the energy region of 2 eV/u to 20 keV/u. Results show that the dominant reaction channel is Ne^(+)(2s2p^(6) ^(2)S) + He^(+)(1s) in the considered energy region due to strong couplings with the initial state Ne(2s^(2)2p^(6)^(1)S) + He^(2+) around the internuclear distance of 4.6 a.u. In our calculations, the SEC cross sections decrease initially and then increase whereby, the minimum point is around 0.38 keV/u with the increase of collision energies. After considering the effects of the electron translation factor(ETF), the SEC cross sections are increased by 15%–25% nearby the energy region of keV/u and agree better with the available results. The DEC cross sections are smaller than those of SEC because of the larger energy gaps and no strong couplings with the initial state. Due to the Demkov-type couplings between DEC channel Ne^(2+)(2s^(2)2p^(4)^(1)S) + He(1s^(2)) and the dominating SEC channel Ne^(+)(2s2p^(6) ^(2)S) + He^(+)(1s), the DEC cross sections increase with increasing impact energies. Good consistency can also be found between the present DEC and the experimental measurements in the overlapping energy region.

关键词： SEC DEC Ab Initio Study of Single-and Double-Electron Capture Processes in Collisions of He Ions and Ne Atoms

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Protein Folding as a Jamming Transition

PRX Life

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PRX Life 2025年第1期3卷 013018-013018页

作者： Alex T. Grigas Zhuoyi Liu Jack A. Logan Mark D. Shattuck Corey S. O'Hern Graduate Program in Computational Biology and Biomedical Informatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

Proteins fold to a specific functional conformation with a densely packed core that controls their stability. Despite their importance, we lack a quantitative explanation for why all protein cores, regardless of their overall fold, possess the same average packing fraction 〈ϕ〉≈0.55. However, important developments in the physics of jamming in particulate systems can shed light on the packing of protein cores. Here, we extend the framework of jamming to describe core packing in collapsed polymers, as well as in all-atom models of folded proteins. First, we show in a spherical bead-spring polymer model (with and without bond-angle constraints) that as the hydrophobic interactions increase relative to thermal fluctuations, a jamming-like transition occurs when the core packing fraction exceeds ϕc with the same power-law scaling behavior for the potential energy Vr, excess contact number ΔN, and characteristic frequency of the vibrational density of states ω* versus Δϕ=ϕ−ϕc as that for jammed particulate systems. Then, we develop an all-atom model for proteins and find that, above ϕc∼0.55, protein cores undergo a jamming-like transition, but with anomalous power-law scaling for Vr, ΔN, and ω* versus Δϕ. The all-atom protein model remains close to the native protein structure during jamming and accurately refolds from partially unfolded states.

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Quench characteristics and mechanical responses during quench propagation in rare earth barium copper oxide pancake coils

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applied mathematics and Mechanics(English Edition) 2021年第2期42卷 235-250页

作者： Mengdie NIU Jing XIA Huadong YONG Youhe ZHOU Key Laboratory of Mechanics on Disaster and Environment in Western China The Ministry of Education of ChinaLanzhou UniversityLanzhou 730000China Department of Mechanics and Engineering Sciences College of Civil Engineering and MechanicsLanzhou UniversityLanzhou 730000China Institute of Applied Physics and Computational Mathematics Beijing 100094China

Quench and mechanical behaviors are critical issues in high temperature superconducting(HTS)*** this paper,the quench characteristics in the rare earth barium copper oxide(REBCO)pancake coil at 4.2K are analyzed,and a two-dimensional(2D)axisymmetric electro-magneto-thermal model is *** effects of the constituent materials,background field,and coil size are *** elastoplastic mechanical model is used to study the corresponding mechanical responses during the quench *** variations of the temperature and strain in superconducting layers are *** results indicate that the radial strain evolutions can reflect the transverse quench propagation and the tensile hoop and radial stresses in superconducting layers increase with the quench *** possible damages are discussed with the consideration of the effects of the background field and coil *** is concluded that the high background field significantly increases the maximum tensile hoop and radial stresses in quenching coils and local damage may be caused.

关键词： rare earth barium copper oxide(REBCO)pancake coil hoop stress quench characteristic mechanical response radial stress

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Generalized nonbacktracking bounds on the influence in independent cascade models

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2020年第1期21卷 1112-1147页

作者： Emmanuel Abbe Sanjeev Kulkarni Eun Jee Lee Program in Applied and Computational Mathematics and Department of Electrical Engineering Princeton University Princeton NJ Department of Electrical Engineering Princeton University Princeton NJ Program in Applied and Computational Mathematics Princeton University Princeton NJ

This paper develops deterministic upper and lower bounds on the influence measure in a network, more precisely, the expected number of nodes that a seed set can influence in the independent cascade model. In particular, our bounds exploit r-nonbacktracking walks and Fortuin--Kasteleyn--Ginibre (FKG) type inequalities, and are computed by message passing algorithms. Further, we provide parameterized versions of the bounds that control the trade-off between efficiency and accuracy. Finally, the tightness of the bounds is illustrated on various network models.

关键词： influence estimation nonbacktracking walk message passing social networks independent cascade model

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A New Time-Based Iterative Solver for Linear Standing-Wave Problems

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Journal of Scientific Computing 1999年第4期14卷 329-346页

作者： Ganguly, Kishor Orszag, Steven A. Program in Applied and Computational Mathematics Princeton University USA Department of Mathematics Yale University New Haven

We explore time-based solvers for linear standing-wave problems, especially the oscillatory Helmholtz equation. Here, we show how to accelerate the convergence properties of timestepping. We introduce a new time-based solver that we call phase-adjusted time-averaging (PATA), which we couple to timestepping to form the PATA-TS solver. Numerical experiments indicate that the PATA-TS solver is faster than the PATA solver and timestepping by a factor of 1.2 and 1.5 or more, respectively. We also explain why the PATA-TS solver is robust, efficient, and easy to program for a variety of practical applications.

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Positron-Impact Excitation of Hydrogen Atoms in Debye Plasmas

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Chinese physics Letters 2010年第1期27卷 111-114页

作者：张松斌祁月盈屈一至陈向军王建国 Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics University of Science and Technology of China Hefei 230026 Key Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics PO Box 8009 Beijing 100088 School of Electrical Engineering Jiaxing University Jiaxing 314001 College of Material Sciences and Optoelectronic Technology Graduate School of the Chinese Academy of Sciences PO Box 4588 Beijing 100049

The positron-impact excitation of hydrogen atoms embedded in plasma environments is investigated using the close-coupling approximation from the low to intermediate energy region without including any positronium formation channel, and the excitation cross sections for 1s→2s, 1s→2p and 2s→2p processes are calculated in a wide Debye parameter range. The screening interactions, described by the Debye-Hückel model, decrease the coupling matrix elements, resulting in the reduction of the excitation cross sections from a few percent to one magnitude of ten. This will alter remarkably the spectroscopy of hydrogen in intensity and position, which should be considered in the simulation and diagnostics under some specific plasma conditions.

关键词： Chinese climate network complex systems small world community

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Second-order time evolution scheme for time-dependent neutron transport equation

Second-order time evolution scheme for time-dependent neutro...

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作者： Hong, Zhenying Yuan, Guangwei Fu, Xuedong Yang, Shulin Institute of Applied Physics and Computational Mathematics Department 6 NO.2. Fenghaodong Road Haidian District Beijing 100094 China

In this paper, the typical exponential method, diamond difference and modified time discrete scheme is researched for self adaptive time step. The second-order time evolution scheme is applied to time-dependent spherical neutron transport equation by discrete ordinates method. The numerical results show that second-order time evolution scheme associated exponential method has some good properties. The time differential curve about neutron current is more smooth than that of exponential method and diamond difference and modified time discrete scheme.

关键词： Diamonds

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Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes

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BMC Research Notes 2009年第1期2卷 1-11页

作者： Grover, Dhruv Yang, Junsheng Ford, Daniel Tavaré, Simon Tower, John Molecular and Computational Biology Program Department of Biological Sciences University of Southern California Los Angeles CA 90089-2910 United States Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge CB3 0WA United Kingdom

Background. Fluorescent proteins such as GFP (Green Fluorescent Protein) and DsRED (Discosoma *** Fluorescent Protein) are often used as reporter molecules for transgene expression in Drosophila and other species. We have recently reported methods that allow simultaneous tracking of animal movement and GFP expression in real time, however the assay was limited to single animals and a single transgene. Numerous studies would be facilitated by methods that allow for assay of multiple animals and multiple transgenes. Findings. Here we report an improved fly video tracking system that allows multiple transgenic flies to be tracked simultaneously using visible light, GFP fluorescence and DsRED fluorescence. The movement of multiple flies could be accurately tracked at real time rates, while simultaneously assaying the expression level of two different transgenes marked with GFP and DsRED. The individual flies could be accurately tracked and distinguished even during periods when transgene fluorescence was undetected. For example, characteristic patterns of hsp70 and hsp22 transgene induction could be simultaneously quantified and correlated with animal movement in aging flies, and as groups of flies died due to dessication/starvation. Conclusion. The improved methods allow for more efficient assay of the correlation between gene expression, behavior, aging and mortality: multiple animals can be assayed with simultaneous quantification of multiple transgenes using GFP and DsRED fluorescence. These methods should allow for increased flexibility in experimental designs. For example, in the future it should be possible to use gene expression levels to predict remaining life span more accurately, and to quantify gene expression changes caused by interactions between animals in real time. © 2009 Tower et al.

关键词： Green Fluorescent Protein Extended Kalman Filter Green Fluorescent Protein Expression Green Fluorescent Protein Fluorescence Daily Activity Pattern

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A third-order moving mesh cell-centered scheme for one-dimensional elastic-plastic flows

arXiv

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arXiv 2017年

作者： Cheng, Jun-Bo Huang, Weizhang Jiang, Song Tian, Baolin Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China Department of Mathematics University of Kansas LawrenceKS66045 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China

A third-order moving mesh cell-centered scheme without the remapping of physical variables is developed for the numerical solution of one-dimensional elastic-plastic flows with the Mie-Grüneisen equation of state, the Wilkins constitutive model, and the von Mises yielding criterion. The scheme combines the Lagrangian method with the MMPDE moving mesh method and adaptively moves the mesh to better resolve shock and other types of waves while preventing the mesh from crossing and tangling. It can be viewed as a direct arbitrarily Lagrangian-Eulerian method but can also be degenerated to a purely Lagrangian scheme. It treats the relative velocity of the fluid with respect to the mesh as constant in time between time steps, which allows high-order approximation of free boundaries. A time dependent scaling is used in the monitor function to avoid possible sudden movement of the mesh points due to the creation or diminishing of shock and rarefaction waves or the steepening of those waves. A two-rarefaction Riemann solver with elastic waves is employed to compute the Godunov values of the density, pressure, velocity, and deviatoric stress at cell interfaces. Numerical results are presented for three examples. The third-order convergence of the scheme and its ability to concentrate mesh points around shock and elastic rarefaction waves are demonstrated. The obtained numerical results are in good agreement with those in literature. The new scheme is also shown to be more accurate in resolving shock and rarefaction waves than an existing third-order cell-centered Lagrangian scheme.65N08, 76M12 Copyright © 2017, The Authors. All rights reserved.

关键词： Elastoplasticity

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