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DeePMD-kit v2: A software package for Deep Potential models

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

Modeling the evolution of COVID-19 via compartmental and particle-based approaches: Application to the Cyprus case

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arXiv 2020年

作者： Alexandrou, Constantia Harmandaris, Vangelis Irakleous, Anastasios Koutsou, Giannis Savva, Nikos Department of Physics University of Cyprus P/O/ Box 20537 Nicosia1678 Cyprus Computation-based Science and Technology Research Center The Cyprus Institute 20 Constantinou Kavafi Str. Nicosia2121 Cyprus Department of Mathematics and Applied Mathematics University of Crete Institute of Applied and Computational Mathematics FORTH HeraklionGR-71110 Greece

We present two different approaches for modeling the spread of the COVID-19 pandemic. Both approaches are based on the population classes susceptible, exposed, infectious, quarantined, and recovered and allow for an arbitrary number of subgroups with different infection rates and different levels of testing. The first model is derived from a set of ordinary differential equations that incorporates the rates at which population transitions take place among classes. The other is a particle model, which is a specific case of crowd simulation model, in which the disease is transmitted through particle collisions and infection rates are varied by adjusting the particle velocities. The parameters of these two models are tuned using information on COVID-19 from the literature and country-specific data, including the effect of restrictions as they were imposed and lifted. We demonstrate the applicability of both models using data from Cyprus, for which we find that both models yield very similar results, giving confidence in the predictions. Copyright © 2020, The Authors. All rights reserved.

关键词： Ordinary differential equations

Recollision of excited electron in below-threshold nonsequential double ionization

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arXiv 2021年

作者： Hao, Xiaolei Bai, Yuxing Li, Chan Zhang, Jingyu Li, Weidong Yang, Weifeng Liu, MingQing Chen, Jing Institute of Theoretical Physics Department of Physics State Key Laboratory of Quantum Optics and Quantum Optics Devices Collaborative Innovation Center of Extreme Optics Shanxi University Taiyuan030006 China Department of Physics College of Science Shantou University Shantou Guangdong515063 China Institute of Applied Physics and Computational Mathematics P. O. Box 8009 Beijing100088 China Shenzhen Key Laboratory of Ultraintense Laser and Advanced Material Technology Center for Advanced Material Diagnostic Technology College of Engineering Physics Shenzhen Technology University Shenzhen518118 China

Consensus has been reached that recollision, as the most important post-tunneling process, is responsible for nonsequential double ionization process in intense infrared laser field, however, its effect has been restricted to interaction between the first ionized electron and the residual univalent ion so far. Here we identify the key role of recollision between the second ionized electron and the divalent ion in the below-threshold nonsequential double ionization process by introducing a Coulomb-corrected quantum-trajectories method, which enables us to well reproduce the experimentally observed cross-shaped and anti-correlated patterns in correlated two-electron momentum distributions, and also the transition between these two patterns. Being significantly enhanced relatively by the recapture process, recolliding trajectories of the second electron excited by the first- or third-return recolliding trajectories of the first electron produce the cross-shaped or anti-correlated distributions, respectively. And the transition is induced by the increasing contribution of the third return with increasing pulse duration. Our work provides new insight into atomic ionization dynamics and paves the new way to imaging of ultrafast dynamics of atoms and molecules in intense laser field. Copyright © 2021, The Authors. All rights reserved.

关键词： Ionization of gases

Enabling magnetoelectric spin-orbit logic and memory

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Newton 2025年第1期1卷

作者： Sajid Husain Zhi Yao Ramamoorthy Ramesh Department of Materials Science and Engineering University of California Berkeley Berkeley CA 94720 USA Materials Science Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA Department of Physics University of California Berkeley Berkeley CA 94720 USA Department of Physics and Astronomy Rice University Houston TX 77005 USA Department of Materials and Nanoengineering Rice University Houston TX 77005 USA

The interplay between the spin and charge degrees of freedom is an extremely exciting area of research, from both a fundamental science and an applications perspective, and it has the potential to revolutionize the world of computing. However, realizing this potential requires a multitude of breakthroughs that range from fundamental scientific exploration to practical implementation of these discoveries. In this context, we use a magnetoelectric, spin-orbit-coupled (MESO) device to underscore the critical materials physics challenges, striving to bridge the divide between condensed matter physics and tangible applications. In this review article, through the elucidation of the pivotal role played by magnetoelectric coupling mediated by spin-orbit physics of this device, we aim to catalyze further translational research across the broad materials physics community. We discuss the recent development of MESO and possible routes to solve the existing issues with the materials with open challenges for future research.

关键词： MESO multiferroics magnetoelectric spin-orbit coupling spin charge conversion

Type-II Dirac cones and electron-phonon interaction in monolayer biphenylene from first-principles calculations

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Physical Review B 2021年第23期104卷 235422-235422页

作者： Peng-Fei Liu Jingyu Li Chi Zhang Xin-Hai Tu Junrong Zhang Ping Zhang Bao-Tian Wang David J. Singh Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 China Spallation Neutron Source Science Center Dongguan 523803 China Key Laboratory of Materials Physics Institute of Solid State Physics HFIPS Chinese Academy of Sciences Hefei 230031 China Foshan (Southern China) Institute for New Materials Foshan 528200 Guangdong China College of Electrical Engineering Henan University of Technology Zhengzhou 450001 China School of Physics and Physical Engineering Qufu Normal University Qufu 273165 China LCP Institute of Applied Physics and Computational Mathematics Beijing 100088 China Collaborative Innovation Center of Extreme Optics Shanxi University Taiyuan Shanxi 030006 China Department of Physics and Astronomy University of Missouri Columbia Missouri 65211 USA Department of Chemistry University of Missouri Columbia Missouri 65211 USA

We report a first-principles investigation of electronic structure, topological bands, and electron-phonon interactions in metallic biphenylene sheets. Biphenylene is a recently synthesized sp2-bonded carbon allotrope. We find coupling of electrons at the Fermi surface to very high frequency carbon-derived phonons, analogous to superconducting MgB2. This leads to low-temperature weak coupling superconductivity due to an unusual combination of exceptionally large logarithmically averaged phonon frequency ωlog=1369 K and moderate electron-phonon coupling. The electronic structure shows a two-band Fermi surface dominated by C pz orbitals and a pair of type-II tilted Dirac cones along the Γ-Y line at the Brillouin zone boundary. Berry curvature and edge-state calculations show that monolayer biphenylene is a two-dimensional Z2 topological material. Thus, monolayer biphenylene is predicted to be a topological superconductor based on C p orbitals and high-frequency phonons.

关键词： Edge states Electron-phonon coupling First-principles calculations Superconductors Topological materials 2-dimensional systems Dirac semimetal BCS theory Density functional theory

Early Detection of Preeclampsia using a Rule-Based System Information System 1

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Early Detection of Preeclampsia using a Rule-Based System In...

1st International Conference on Computer, Science, Engineering and Technology, ICComSET 2018

作者： Aini, F.N. Widyawati, M.N. Suryono, S. Purwokerto Midwifery Program Poltekkes Kemenkes Semarang Indonesia Postgraduate Applied Science Midwifery Program Poltekkes Kemenkes Semarang Indonesia Department of Physics Faculty of Science and Mathematics University Diponegoro Semarang Indonesia

Preeclampsia is the highest cause of maternal death. One program to reduce Maternal Mortality Rate (MMR) is by early detection. The incomplete history of maternal history that has occurred has led to the determination of an incorrect diagnosis and has resulted in errors in decision making. The results of the survey in the detection of preeclampsia include midwives not conducting a history of past medical history, physical examination during the first antenatal care visit is incomplete. During this time the detection and diagnosis model is still done manually, so it was not effective and efficient. The inspection data obtained using the information system becomes more complete and faster. Data obtained with information systems can be seen anywhere and anytime. This study produced innovations for the detection of preeclampsia in pregnant women using a rule-based system information system. This study uses the Quasy experimental posttest-only design. The subjects of this study were 66 pregnant women. Data collection was carried out using questionnaires and checklists. The results showed that early detection of preeclampsia using a rule-based system information system could improve the completeness of data on pregnant women up to 35.66%, and speed up the detection time of preeclampsia up to 35.60%. This system also has an effectivenessvalue 84.8%. © 2019 IOP Publishing Ltd. All rights reserved.

关键词： Decision making

computational Methods for Single-Particle Cryo-EM

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arXiv 2020年

作者： Singer, Amit Sigworth, Fred J. Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Departments of Cellular and Molecular Physiology Biomedical Engineering and Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States

Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging method that does not require crystallization and can capture molecules in their native states. In single-particle cryo-EM, the three-dimensional molecular structure needs to be determined from many noisy two-dimensional tomographic projections of individual molecules, whose orientations and positions are unknown. The high level of noise and the unknown pose parameters are two key elements that make reconstruction a challenging computational problem. Even more challenging is the inference of structural variability and flexible motions when the individual molecules being imaged are in different conformational states. This review discusses computational methods for structure determination by single-particle cryo-EM and their guiding principles from statistical inference, machine learning, and signal processing that also play a significant role in many other data science applications. Copyright © 2020, The Authors. All rights reserved.

关键词： Molecules

Solving the Schrödinger equations for several few lowest energies of H2 using Monte-Carlo method

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AIP Conference Proceedings 2023年第1期2906卷

作者： Teguh Budi Prayitno Marliana Candra Kartika Rui-Qin Zhang Yanoar Pribadi Sarwono Department of Physics Faculty of Mathematics and Natural Science Universitas Negeri Jakarta Kampus A Jl. Rawamangun Muka Jakarta Timur 13220 Indonesia Shenzhen JL Computational Science and Applied Research Institute Shenzhen 518131 China Research Center for Quantum Physics National Research and Innovation Agency (BRIN) Tangerang Selatan 15314 Indonesia

We calculate the energy of ground state S0 and the first two excited states S1 and T1 of the hydrogen molecule. The corresponding wave function is expanded with the bonding and non-bonding molecular orbitals where each hydrogen atom is represented with one unoptimized Slater type basis function, then all integrations for the energy components evaluations are performed and estimated with the Monte-Carlo method. Unlike the standard method of the Hartree-Fock, the construction of the Fock matrix followed with its diagonalization is circumvented. For considerably large data samplings of 50, 000, the computational time is still cheap, costing just a split of second. At the STO-3G level of theory, the ground state energies show similar accuracy with the Hartree-Fock calculations while superior accuracy for the singlets and triplets reveal with ease the electron correlation effect.

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Adaptive optics imaging with a pyramid wavefront sensor for visual science

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arXiv 2021年

作者： Brunner, Elisabeth Shatokhina, Julia Shirazi, Muhammad Faizan Drexler, Wolfgang Leitgeb, Rainer Pollreisz, Andreas Hitzenberger, Christoph K. Ramlau, Ronny Pircher, Michael Center for Medical Physics and Biomedical Engineering Medical University of Vienna Waehringer Guertel 18-20 ViennaA-1090 Austria Johann Radon Institute for Computational and Applied Mathematics Altenbergerstrasse 69 LinzA-4040 Austria Department of Ophthalmology and Optometry Medical University of Vienna Waehringer Guertel 18-20 ViennaA-1090 Austria Johannes Kepler University Linz Industrial Mathematics Institute Altenbergerstrasse 69 LinzA-4040 Austria

The pyramid wavefront sensor (P-WFS) has replaced the Shack-Hartmann (SH-) WFS as sensor of choice for high performance adaptive optics (AO) systems in astronomy because of its flexibility in pupil sampling, its dynamic range, and its improved sensitivity in closed-loop application. Usually, a P-WFS requires modulation and high precision optics that lead to high complexity and costs of the sensor. These factors limit the competitiveness of the P-WFS with respect to other WFS devices for AO correction in visual science. Here, we present a cost effective realization of AO correction with a non-modulated P-WFS and apply this technique to human retinal in vivo imaging using optical coherence tomography (OCT). P-WFS based high quality AO imaging was, to the best of our knowledge for the first time, successfully performed in 5 healthy subjects and benchmarked against the performance of conventional SH-WFS based AO. Smallest retinal cells such as central foveal cone photoreceptors are visualized and we observed a better quality of the images recorded with the P-WFS. The robustness and versatility of the sensor is demonstrated in the model eye under various conditions and in vivo by high-resolution imaging of other structures in the retina using standard and extended fields of view. Copyright © 2021, The Authors. All rights reserved.

关键词： Adaptive optics