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arXiv 2021年

作者： Maher, Charles Emmett Stillinger, Frank H. Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Dense, disordered packings of particles are useful models of low-temperature amorphous phases of matter, biological systems, granular media, and colloidal systems. The study of dense packings of nonspherical particles enables one to ascertain how rotational degrees of freedom affect packing behavior. Here, we study superballs, a large family of deformations of the sphere, defined in three dimensions by |x1|2p + |x2|2p + |x3|2p ≤ 1, where p ∈ (0, ∞) is a deformation parameter indicating to what extent the shape deviates from a sphere. As p increases from the sphere point (p = 1), the superball tends to a cuboidal shape and approaches a cube in the p → ∞ limit. As p → 0.5, it approaches an octahedron, becomes a concave body with octahedral symmetry for p ¯) vary nonanalytically as p diverges from unity. Here, we use an event-driven molecular dynamics algorithm to produce MRJ superball packings with 0.85 ≤ p ≤ 1.50. To supplement the previous work on such packings, we characterize their large-scale structure by examining the behaviors of their structure factors S(Q) and spectral densities χV (Q), as the wave number Q tends to zero, and find that these packings are effectively hyperuniform for all values of p examined. We show that the mean width w¯ is a useful length scale to make distances dimensionless in order to compare systematically superballs of different shape. Moreover, we compute the complementary cumulative pore-size distribution F (δ) and find that the pore sizes tend to decrease as |1 − p| increases. From F (δ), we estimate how the fluid permeability, mean survival time, and principal diffusion relaxation time vary as a function of p. Additionally, we compute the diffusion "spreadability" S(t) [Torquato, Phys. Rev. E, 104, 054102, (2021)] of these packings and find that the long-time power-law scaling indicates these packings are hyperuniform with a small-Q power law scaling of the spectral density χV (Q) ∼ Qα with an exponent α that ranges from 0.64 at th

关键词： Spheres

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Modeling subgrid-scale forces by spatial artificial neural networks in large eddy simulation of turbulence

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Physical Review Fluids 2020年第5期5卷 054606-054606页

作者： Chenyue Xie Jianchun Wang Weinan E Shenzhen Key Laboratory of Complex Aerospace Flows Center for Complex Flows and Soft Matter Research Department of Mechanics and Aerospace Engineering Southern University of Science and Technology Shenzhen 518055 People's Republic of China Department of Mathematics Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Spatial artificial neural network (ANN) models are developed for subgrid-scale (SGS) forces in the large eddy simulation (LES) of turbulence. The input features are based on the first-order derivatives of the filtered velocity field at different spatial locations. The correlation coefficients of SGS forces predicted by the spatial artifical neural network (SANN) models with reasonable spatial stencil geometry can be made larger than 0.99 in an a priori analysis, and the relative error of SGS forces can be made smaller than 15%, much smaller than that of the traditional gradient model. In a posteriori analysis, a detailed comparison is made on the results of LES using the SANN model, implicit large eddy simulation (ILES), the dynamic Smagorinsky model (DSM), and the dynamic mixed model (DMM) at grid resolution of 643. It is shown that the SANN model performs better than the ILES, DSM, and DMM models in the prediction of the spectrum and other statistical properties of the velocity field, as well as the instantaneous flow structures. These results suggest that artificial neural network with consideration of spatial characteristics is a very effective tool for developing advanced SGS models in LES of turbulence.

关键词： Compressible flows Turbulence Artificial neural networks

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The underestimation of high pressure in DFT+U simulation for the wide range cold-pressure of lanthanide metals

arXiv

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arXiv 2021年

作者： Wang, Yue-Chao Liu, Bei-Lei Liu, Yu Liu, Hai-Feng Bi, Yan Gao, Xing-Yu Sheng, Jie Song, Hong-Zhou Tian, Ming-Feng Song, Hai-Feng Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China School of Mathematical Sciences Beijing Normal University Beijing100875 China Center for High Pressure Science and Technology Advanced Research Beijing100094 China National Key Laboratory for Shock Wave and Detonation Physics Institute of Fluid Physics CAEP Mianyang621900 China Graduate School of China Academy of Engineering Physics Beijing100088 China

Density functional theory plus U (DFT+U) is one of the most efficient first-principles methods to simulate the cold pressure properties of strongly-correlated materials. However, the applicability of DFT+U at ultra-high pressure is not sufficiently studied, especially in the widely-used augmented schemes [such as projector augmented wave (PAW) and linearized augmented plane wave (LAPW)]. This work has systematically investigated the performance of DFT+U in PAW and LAPW at the pressure up to several hundred GPa for the lanthanide metals, which is a typical strongly-correlated series. We found DFT+U simulation in PAW exhibits an unphysical underestimation of pressure in high-pressure region, which was not observed in conventional DFT simulation. By delicate analysis and comparison with local-orbital-independent hybrid functional results, we have demonstrated that this unphysical behavior is related to a normalization problem on the local density matrix caused by the overlap of local orbitals in PAW under high pressure. Additionally, we observed a slight underestimating of pressure in correlation correction methods in heavy lanthanides (Tm, Yb and Lu) in high-pressure region comparing with the DFT results without the influence of local orbital overlap, and it might be related to the enhancement of binding between atoms in correlation correction methods at high pressure. Our work reveals the underestimation of high pressure in DFT+U simulation, analyses two sources of this unusual behavior and proposes their mechanism. Most importantly, our investigation highlights the breakdown of DFT+U for high pressure simulation in VASP package based on PAW framework. Copyright © 2021, The Authors. All rights reserved.

关键词： Density functional theory

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Semiclassical Trajectory Perspective of Glory Rescattering in Strong-field Photoelectron Holography

arXiv

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arXiv 2021年

作者： Liao, L.G. Xia, Qinzhi Z. Cai, J. Liu, J. School of Physics Peking University Beijing100871 China CAPT HEDPS IFSA Collaborative Innovation Center of MoE Peking University Beijing100871 China National Laboratory of Science and Technology on Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China School of Physics and Electronic Engineering Jiangsu Normal University Xuzhou221116 China Graduate School of China Academy of Engineering Physics Beijing100193 China

We investigate theoretically the photoelectron momentum distribution (PMD) of the ionized atoms irradiated by a linearly polarized intense laser, focusing on the holography interference patterns in PMD that carry important information of the initial wavefunction of a tunneled electron and its experienced atomic potential in rescattering. With the help of Dyson series and semiclassical propagator, we calculate the scattering amplitudes in the cylindrical coordinate representation. In contrast to conventional recognitions that the photoelectron holography is the interference of two branches of electron trajectories, however, we find strikingly that infinite semiclassical trajectories can be deflected by the combined Coulomb potential and laser field into the same final momentum: The initial momenta are found to be distributed on a ring-shape curve in the transverse momentum plane and the initial positions of these trajectories are perpendicular to their initial momentum vectors. For the zero final transverse momentum, the above ring-source trajectories degenerate into the point-source axial caustic trajectories (or Glory trajectories) and the quantum interference of these trajectories will dramatically alter the scattering amplitudes that is termed as Glory rescattering effect. With following Berry's spirit of uniform approximation for Glory scattering in optics, we can finally derive a uniform formulation of the rescattering amplitude in the Bessel functions for the strong-field photoelectron holography (SFPH) patterns. Our results are in good agreement with solutions of the time-dependent Schrödinger equation and can account for recent photoelectron holography experiments. Important applications of our theory are also discussed. Copyright © 2021, The Authors. All rights reserved.

关键词： Trajectories

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Gap sensitivity reveals universal behaviors in optimized photonic crystal and disordered networks

arXiv

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arXiv 2021年

作者： Klatt, Michael Andreas Steinhardt, Paul J. Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Institut für Theoretische Physik University of Erlangen-Nürnberg Staudtstr. 7 Erlangen91058 Germany Department of Chemistry Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Through an extensive series of high-precision numerical computations of the optimal complete photonic band gap (PBG) as a function of dielectric contrast α for a variety of crystal and disordered heterostructures, we reveal striking universal behaviors of the gap sensitivity S(α) ≡ d∆(α)/dα, the first derivative of the optimal gap-to-midgap ratio ∆(α). In particular, for all our crystal networks, S(α) takes a universal form that is well approximated by the analytic formula for a one-dimensional quarter-wave stack, SQWS(α). Even more surprisingly, the values of S(α) for our disordered networks converge to SQWS(α) for sufficiently large α. A deeper understanding of the simplicity of this universal behavior may provide fundamental insights about PBG formation and guidance in the design of novel photonic *** Codes 78A48, 78M50 (Primary) 82D25, 82D30, 52C99 (Secondary) © 2021, CC BY-SA.

关键词： Photonic band gap

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Target density effects on charge tansfer of laser-accelerated carbon ions in dense plasma

arXiv

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arXiv 2022年

作者： Ren, Jieru Ma, Bubo Liu, Lirong Wei, Wenqing Chen, Benzheng Zhang, Shizheng Xu, Hao Hu, Zhongmin Li, Fangfang Wang, Xing Yin, Shuai Feng, Jianhua Zhou, Xianming Gao, Yifang Li, Yuan Shi, Xiaohua Li, Jianxing Ren, Xueguang Xu, Zhongfeng Deng, Zhigang Qi, Wei Wang, Shaoyi Fan, Quanping Cui, Bo Wang, Weiwu Yuan, Zongqiang Teng, Jian Wu, Yuchi Cao, Zhurong Zhao, Zongqing Gu, Yuqiu Cao, Leifeng Zhu, Shaoping Cheng, Rui Lei, Yu Wang, Zhao Zhou, Zexian Xiao, Guoqing Zhao, Hongwei Hoffmann, Dieter H.H. Zhou, Weimin Zhao, Yongtao MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter School of Science Xi'an Jiaotong University Xi'An710049 China Science and Technology on Plasma Physics Laboratory Laser Fusion Research Center China Academy of Engineering Physics Mianyang621900 China Advanced Materials Testing Technology Research Center Shenzhen University of Technology Shenzhen518118 China Institute of Applied Physics and Computational Mathematics Beijing100094 China Graduate School China Academy of Engineering Physics Beijing100088 China Institute of Modern Physics Chinese Academy of Sciences Lanzhou710049 China

We report on charge state measurements of laser-accelerated carbon ions in the energy range of several MeV penetrating a dense partially ionized plasma. The plasma was generated by irradiation of a foam target with laser-induced hohlraum radiation in the soft X-ray regime. We used the tri-cellulose acetate (C9H16O8) foam of 2 mg/cm−3 density, and 1-mm interaction length as target material. This kind of plasma is advantageous for high-precision measurements, due to good uniformity and long lifetime compared to the ion pulse length and the interaction duration. The plasma parameters were diagnosed to be Te=17 eV and ne=4 × 1020 cm−3. The average charge states passing through the plasma were observed to be higher than those predicted by the commonly-used semiempirical formula. Through solving the rate equations, we attribute the enhancement to the target density effects which will increase the ionization rates on one hand and reduce the electron capture rates on the other hand. In previsous measurement with partially ionized plasma from gas discharge and z-pinch to laser direct irradiation, no target density effects were ever demonstrated. For the first time, we were able to experimentally prove that target density effects start to play a significant role in plasma near the critical density of Nd-Glass laser radiation. The finding is important for heavy ion beam driven high energy density physics and fast ignitions. © 2022, CC BY-NC-ND.

关键词： Irradiation

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Local two-sample testing over graphs and point-clouds by random-walk distributions

arXiv

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arXiv 2020年

作者： Landa, Boris Qu, Rihao Chang, Joseph Kluger, Yuval Program in Applied Mathematics Yale University Department of Pathology Yale University School of Medicine Department of Statistics and Data Science Yale University Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Immunology Yale School of Medicine

Rejecting the null hypothesis in two-sample testing is a fundamental tool for scientific discovery. Yet, aside from concluding that two samples do not come from the same probability distribution, it is often of interest to characterize how the two distributions differ. Given samples from two densities f1and f0, we consider the task of localizing occurrences of the inequality f1> f0. To avoid the challenges associated with high-dimensional space, we propose a general hypothesis testing framework where hypotheses are formulated adaptively to the data by conditioning on the combined sample from the two densities. We then investigate a special case of this framework where the notion of locality is captured by a random walk on a weighted graph constructed over this combined sample. We derive a tractable testing procedure for this case employing a type of scan statistic, and provide non-asymptotic lower bounds on the power and accuracy of our test to detect whether f1> f0in a local sense. Furthermore, we characterize the test's consistency according to a certain problem-hardness parameter, and show that our test achieves the minimax detection rate for this parameter. We conduct numerical experiments to validate our method, and demonstrate our approach on two real-world applications: detecting and localizing arsenic well contamination across the United States, and analyzing two-sample single-cell RNA sequencing data from melanoma *** Codes 62G10 Copyright © 2020, The Authors. All rights reserved.

关键词： Random processes

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Exclusion Volumes of Convex Bodies in High Space Dimensions: Applications to Virial Coefficients and Continuum Percolation

arXiv

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arXiv 2022年

作者： Torquato, Salvatore Jiao, Yang Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Materials Science and Engineering Arizona State University TempeAZ85287 United States Department of Physics Arizona State University TempeAZ85287 United States

Using the concepts of mixed volumes and quermassintegrals of convex geometry, we derive an exact formula for the exclusion volume vex(K) for a general convex body K that applies in any space dimension. While our main interests concern the rotationally-averaged exclusion volume of a convex body with respect to another convex body, we also describe some results for the exclusion volumes for convex bodies with the same orientation. We show that the sphere minimizes the dimensionless exclusion volume vex(K)/v(K) among all convex bodies, whether randomly oriented or uniformly oriented, for any d, where v(K) is the volume of K. When the bodies have the same orientation, the simplex maximizes the dimensionless exclusion volume for any d with a large-d asymptotic scaling behavior of 22d/d3/2, which is to be contrasted with the corresponding scaling of 2d for the sphere. We present explicit formulas for quermassintegrals W0(K), . . ., Wd(K) for many different nonspherical convex bodies, including cubes, parallelepipeds, regular simplices, cross-polytopes, cylinders, spherocylinders, ellipsoids as well as lower-dimensional bodies, such as hyperplates and line segments. These results are utilized to determine the rotationally-averaged exclusion volume vex(K) for these convex-body shapes for dimensions 2 through 12. While the sphere is the shape possessing the minimal dimensionless exclusion volume, we show that, among the convex bodies considered that are sufficiently compact, the simplex possesses the maximal vex(K)/v(K) with a scaling behavior of 21.6618...d. Subsequently, we apply these results to determine the corresponding second virial coefficient B2(K) of the aforementioned hard hyperparticles. Our results are also applied to compute estimates of the continuum percolation threshold ηc derived previously by the authors for systems of identical overlapping convex bodies. We conjecture that overlapping spheres possess the maximal value of ηc among all identical nonzero-vol

关键词： Spheres

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Critical pore radius and transport properties of disordered hard- and overlapping-sphere models

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Physical Review E 2021年第1期104卷 014127-014127页

作者： Michael A. Klatt Robert M. Ziff Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Institut für Theoretische Physik FAU Erlangen-Nürnberg Staudtstr. 7 91058 Erlangen Germany Center for the Study of Complex Systems and Department of Chemical Engineering University of Michigan Ann Arbor Michigan 48109 USA Department of Chemistry Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Transport properties of porous media are intimately linked to their pore-space microstructures. We quantify geometrical and topological descriptors of the pore space of certain disordered and ordered distributions of spheres, including pore-size functions and the critical pore radius δc. We focus on models of porous media derived from maximally random jammed sphere packings, overlapping spheres, equilibrium hard spheres, quantizer sphere packings, and crystalline sphere packings. For precise estimates of the percolation thresholds, we use a strict relation of the void percolation around sphere configurations to weighted bond percolation on the corresponding Voronoi networks. We use the Newman-Ziff algorithm to determine the percolation threshold using universal properties of the cluster size distribution. The critical pore radius δc is often used as the key characteristic length scale that determines the fluid permeability k. A recent study [Torquato, Adv. Wat. Resour. 140, 103565 (2020)] suggested for porous media with a well-connected pore space an alternative estimate of k based on the second moment of the pore size 〈δ2〉, which is easier to determine than δc. Here, we compare δc to the second moment of the pore size 〈δ2〉, and indeed confirm that, for all porosities and all models considered, δc2 is to a good approximation proportional to 〈δ2〉. However, unlike 〈δ2〉, the permeability estimate based on δc2 does not predict the correct ranking of k for our models. Thus, we confirm 〈δ2〉 to be a promising candidate for convenient and reliable estimates of the fluid permeability for porous media with a well-connected pore space. Moreover, we compare the fluid permeability of our models with varying degrees of order, as measured by the τ order metric. We find that (effectively) hyperuniform models tend to have lower values of k than their nonhyperuniform counterparts. Our findings could facilitate the design of porous media with desirable transport properties via targete

关键词： Geophysical networks Materials Patterns in complex systems

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