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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

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Static structural signatures of nearly jammed disordered and ordered hard-sphere packings: Direct correlation function

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Physical Review E 2016年第3期94卷 032902-032902页

作者： Steven Atkinson Frank H. Stillinger Salvatore Torquato Department of Chemistry Department of Physics Princeton Center for Theoretical Science Program of Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

The nonequilibrium process by which hard-particle systems may be compressed into disordered, jammed states has received much attention because of its wide utility in describing a broad class of amorphous materials. While dynamical signatures are known to precede jamming, the task of identifying static structural signatures indicating the onset of jamming have proven more elusive. The observation that compressing hard-particle packings towards jamming is accompanied by an anomalous suppression of density fluctuations (termed “hyperuniformity”) has paved the way for the analysis of jamming as an “inverted critical point” in which the direct correlation function c(r), rather than the total correlation function h(r), diverges. We expand on the notion that c(r) provides both universal and protocol-specific information as packings approach jamming. By considering the degree and position of singularities (discontinuities in the nth derivative) as well as how they are changed by the convolutions found in the Ornstein-Zernike equation, we establish quantitative statements about the structure of c(r) with regards to singularities it inherits from h(r). These relations provide a concrete means of identifying features that must be expressed in c(r) if one hopes to reproduce various details in the pair correlation function accurately and provide stringent tests on the associated numerics. We also analyze the evolution of systems of three-dimensional monodisperse hard spheres of diameter D as they approach ordered and disordered jammed configurations. For the latter, we use the Lubachevsky-Stillinger (LS) molecular dynamics and Torquato-Jiao (TJ) sequential linear programming algorithms, which both generate disordered packings, but can show perceptible structural differences. We identify a short-ranged scaling c(r)∝−1/r as r→0 that accompanies the formation of the delta function at c(D) that indicates the formation of contacts in all cases, and show that this scaling behavior is,

关键词： Jamming

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The phase diagram of a deep potential water model

arXiv

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arXiv 2021年

作者： Zhang, Linfeng Wang, Han Car, Roberto Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China Department of Chemistry Department of Physics Program in Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50 GPa, excluding the vapor stability region. The computational efficiency of the model makes it possible to predict its phase diagram using molecular dynamics. Satisfactory overall agreement with experimental results is obtained. The fluid phases, molecular and ionic, and all the stable ice polymorphs, ordered and disordered, are predicted correctly, with the exception of ice III and XV that are stable in experiments, but metastable in the model. The evolution of the atomic dynamics upon heating, as ice VII transforms first into ice VII′′ and then into an ionic fluid, reveals that molecular dissociation and breaking of the ice rules coexist with strong covalent fluctuations, explaining why only partial ionization was inferred in experiments. © 2021, CC BY-NC-ND.

关键词： Phase diagrams

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A Runge Kutta Discontinuous Galerkin Method for Lagrangian Compressible Euler Equations in Two-Dimensions

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Communications in computational Physics 2014年第4期15卷 1184-1206页

作者： Zhenzhen Li Xijun Yu Jiang Zhu Zupeng Jia School of Mathematical Sciences University of Science and Technology of ChinaHefei 230026P.R.China Graduate School China Academy of Engineering PhysicsBeijing 100088P.R.China Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing 100088P.R.China National Laboratory for Scientific Computing LNCC/MCTIAvenida Getúlio Vargas 33325651-075 PetrópolisRJBrazil

This paper presents a new Lagrangian type scheme for solving the Euler equations of compressible gas *** this new scheme the system of equations is discretized by Runge-Kutta Discontinuous Galerkin(RKDG)method,and the mesh moves with the fluid *** scheme is conservative for the mass,momentum and total energy and maintains second-order *** scheme avoids solving the geometrical part and has free *** of some numerical tests are presented to demonstrate the accuracy and the non-oscillatory property of the scheme.

关键词： Lagrangian type scheme compressible Euler equations RKDG method conservative scheme

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Survival window for atomic tunneling ionization with elliptically polarized laser fields

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Physical Review A 2013年第3期87卷 033415-033415页

作者： Kai-yun Huang Qin-zhi Xia Li-Bin Fu National Laboratory of Science and Technology on Computational Physics Institute of Applied Physics and Computational Mathematics Beijing 100088 China Graduate School China Academy of Engineering Physics Beijing 100088 China HEDPS Center for Applied Physics and Technology Peking University Beijing 100084 China

We find a fraction of atoms remain unionized after the laser pulse when the tunneled electrons are released in a certain window of initial field phase and transverse velocity. The survival window shifts with laser polarization ellipticity and its width varies with respect to laser intensity and atomic ionization potential. Neutral atom yield can be calculated by summing up tunneling probabilities in the window. Our theory can quantitatively reproduce the distribution of the survival yields vs laser ellipticity observed for helium in experiment. For other atom species with smaller ionization potential such as magnesium, our theory predicts a wider distribution than the strong-field approximation model while closer to the three-dimensional semiclassical electron ensemble simulations, indicating the important role of the Coulomb effects.

关键词： TUNNELING (Physics) IONIZATION (Atomic physics) POLARIZATION (Nuclear physics) LASERS in physics LASER pulses PHYSICS experiments POTENTIAL theory (Physics)

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Monte Carlo simulation of prompt γ-ray spectra from depleted uranium under D-T neutron irradiation and electron recoil spectra in a liquid scintillator detector

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Chinese Physics C 2016年第3期40卷 115-119页

作者：秦建国赖财锋刘荣朱通华张信威叶邦角 Department of Modern Physics University of Science and Technology of China Hefei 230026 China Institute of Nuclear Physics and Chemistry China Academy of Engineering Physics P.O.Box 213 Mianyang 621900 China Graduate School China Academy of Engineering Physics Mianyang 621900 China Institute of Applied Physics and Computational Mathematics P.O.Box 8009 Beijing 100088 China

To overcome the problem of inefficient computing time and unreliable results in MCNP5 calculation, a two-step method is adopted to calculate the energy deposition of prompt γ-rays in detectors for depleted uranium spherical shells under D-T neutron irradiation. In the first step, the γ-ray spectrum for energy below 7 MeV is calculated by MCNP5 code; secondly, the electron recoil spectrum in a BC501 A liquid scintillator detector is simulated based on EGSnrc Monte Carlo Code with the γ-ray spectrum from the first step as input. The comparison of calculated results with experimental ones shows that the simulations agree well with experiment in the energy region 0.4–3 MeV for the prompt γ-ray spectrum and below 4 MeVee for the electron recoil spectrum. The reliability of the two-step method in this work is validated.

关键词： Monte Carlo simulation depleted uranium prompt γ-ray energy spectrum recoil electron spectrum

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Domain Formation in the Plasma Membrane: Roles of Nonequilibrium Lipid Transport and Membrane Proteins

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Physical Review Letters 2008年第17期100卷 178102-178102页

作者： Jun Fan Maria Sammalkorpi Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Compositional lipid domains (“lipid rafts”) in plasma membranes are believed to be important components of many cellular processes. The mechanisms by which cells regulate the sizes and lifetimes of these spatially extended domains are poorly understood at the moment. Here we show that the competition between phase separation in an immiscible lipid system and active cellular lipid transport processes naturally leads to the formation of such domains. Furthermore, we demonstrate that local interactions with immobile membrane proteins can spatially localize the rafts and lead to further clustering.

关键词： Lipids

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Influence of nonequilibrium lipid transport, membrane compartmentalization, and membrane proteins on the lateral organization of the plasma membrane

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Physical Review E 2010年第1期81卷 011908-011908页

Compositional lipid domains (lipid rafts) in plasma membranes are believed to be important components of many cellular processes. The mechanisms by which cells regulate the sizes, lifetimes, and spatial localization of these domains are rather poorly understood at the moment. We propose a robust mechanism for the formation of finite-sized lipid raft domains in plasma membranes, the competition between phase separation in an immiscible lipid system and active cellular lipid transport processes naturally leads to the formation of such domains. Simulations of a continuum model reveal that the raft size distribution is broad and the average raft size is strongly dependent on the rates of cellular and interlayer lipid transport processes. We demonstrate that spatiotemporal variations in the recycling may enable the cell to localize larger raft aggregates at specific parts along the membrane. Moreover, we show that membrane compartmentalization may further facilitate spatial localization of the raft domains. Finally, we demonstrate that local interactions with immobile membrane proteins can spatially localize the rafts and lead to further clustering.

关键词： Cell membranes

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Comprehensive analysis of compositional interface fluctuations in planar lipid bilayer membranes

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Physical Review E 2011年第5期84卷 051903-051903页

作者： Tao Han Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

In this paper we present a comprehensive analysis of line tension-driven compositional interface fluctuations in planar lipid bilayer membranes. Our starting point is the advective Cahn-Hilliard equation for the local lipid composition in symmetric membranes, which explicitly incorporates both advective and diffusive lipid transport processes, and which is coupled to the continuum hydrodynamic equations governing the flow behavior of the membrane and surrounding solvent with finite subphase thickness. In order to extract the interface dynamics from the continuum phase-field formalism, we first derive the appropriate sharp-interface limit equations. We then carry out a linear perturbation analysis for the relaxational dynamics of small-amplitude sinusoidal interface fluctuations to yield the general dispersion relation ωk as a function of perturbation wave number k. The resulting expression incorporates the effects of diffusive and advective lipid transport processes within the membrane, viscous or viscoelastic membrane properties, coupling between membrane and solvent, and inertial effects within the membrane and solvent. It is shown that previously considered scenarios naturally emerge as limiting cases of the general result. Furthermore, we discuss two additional scenarios amenable to analysis, one in which the inertia of the solvent is relevant, and another one in which the membrane displays significant viscoelastic properties. Finally, we numerically evaluate the general dispersion relation for three representative model membrane systems.

关键词： BILAYER lipid membranes FLUCTUATIONS (Physics) PERTURBATION (mathematics) VISCOELASTICITY HYDRODYNAMICS

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Hydrodynamic interaction between overlapping domains during recurrence of registration within planar lipid bilayer membranes

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Physical Review E 2014年第3期89卷 032717-032717页

作者： Tao Han Trevor P. Bailey Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Due to a thermodynamic coupling between the two leaflets comprising a lipid bilayer, compositional lipid domains residing within opposing leaflets are often found in registry. If the system is perturbed by displacing one domain relative to the other, diffusive and advective lipid fluxes are established to restore equilibrium and reestablish domain overlap. In this work, we focus on the advective part of the process, and first derive an analytical expression for the hydrodynamic drag coefficient associated with the advective flow for the special case of perfect domain overlap. The resulting expression identifies parameter regions where sliding friction between the leaflets dominates over viscous dissipation within the leaflets or vice versa. It is shown that in all practically relevant cases, sliding friction between the leaflets is the dominant factor. Finally, we investigate the domain separation dependence of the hydrodynamic drag coefficient via direct simulations of a continuum diffuse interface model, and provide useful empirical expressions for its behavior.

关键词： HYDRODYNAMICS BILAYER lipid membranes DRAG coefficient ENERGY dissipation SLIDING friction FLUX (Energy)

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