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Atomistic insights into the nanosecond long amorphization and crystallization cycle of nanoscale Ge2Sb2Te5: An ab initio molecular dynamics study

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Physical Review materials 2018年第4期2卷 043401-043401页

作者： Paulo S. Branicio Kewu Bai H. Ramanarayan David T. Wu Michael B. Sullivan David J. Srolovitz Mork Family Department of Chemical Engineering and Materials Science University of Southern California Los Angeles California 90089 USA Institute of High Performance Computing Agency for Science Technology and Research 1 Fusionopolis Way 16-16 Connexis 138632 Singapore Departments of Materials Science and Engineering & Mechanical Engineering and Applied Mechanics University of Pennsylvania Philadelphia Pennsylvania 19104 USA

The complete process of amorphization and crystallization of the phase-change material Ge2Sb2Te5 is investigated using nanosecond ab initio molecular dynamics simulations. Varying the quench rate during the amorphization phase of the cycle results in the generation of a variety of structures from entirely crystallized (−0.45 K/ps) to entirely amorphized (−16 K/ps). The 1.5-ns annealing simulations indicate that the crystallization process depends strongly on both the annealing temperature and the initial amorphous structure. The presence of crystal precursors (square rings) in the amorphous matrix enhances nucleation/crystallization kinetics. The simulation data are used to construct a combined continuous-cooling-transformation (CCT) and temperature-time-transformation (TTT) diagram. The nose of the CCT-TTT diagram corresponds to the minimum time for the onset of homogenous crystallization and is located at 600 K and 70 ps. That corresponds to a critical cooling rate for amorphization of −4.5 K/ps. The results, in excellent agreement with experimental observations, suggest that a strategy that utilizes multiple quench rates and annealing temperatures may be used to effectively optimize the reversible switching speed and enable fast and energy-efficient phase-change memories.

关键词： Diffusion First-principles calculations Microstructure Temperature Thermodynamics

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Plato’s cube and the natural geometry of fragmentation

arXiv

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arXiv 2019年

作者： Domokos, Gábor Jerolmack, Douglas J. Kun, Ferenc Török, János MTA-BME Morphodynamics Research Group Budapest University of Technology and Economics Budapest Hungary Department of Mechanics Materials and Structure Budapest University of Technology and Economics Budapest Hungary Department of Earth and Environmental Science University of Pennsylvania Philadelphia United States Mechanical Engineering and Applied Mechanics University of Pennsylvania Philadelphia United States Department of Theoretical Physics University of Debrecen Debrecen Hungary Department of Theoretical Physics Budapest University of Technology and Economics Budapest Hungary

Plato envisioned Earth’s building blocks as cubes, a shape rarely found in nature. The solar system is littered, however, with distorted polyhedra — shards of rock and ice produced by ubiquitous fragmentation. We apply the theory of convex mosaics to show that the average geometry of natural 2D fragments, from mud cracks to Earth’s tectonic plates, has two attractors: "Platonic" quadrangles and "Voronoi" hexagons. In 3D the Platonic attractor is dominant: remarkably, the average shape of natural rock fragments is cuboid. When viewed through the lens of convex mosaics, natural fragments are indeed geometric shadows of Plato’s forms. Simulations show that generic binary breakup drives all mosaics toward the Platonic attractor, explaining the ubiquity of cuboid averages. Deviations from binary fracture produce more exotic patterns that are genetically linked to the formative stress field. We compute the universal pattern generator establishing this link, for 2D and 3D fragmentation. Copyright © 2019, The Authors. All rights reserved.

关键词： Geometry

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End-to-end symmetry preserving inter-atomic potential energy model for finite and extended systems 32

End-to-end symmetry preserving inter-atomic potential energy...

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32nd Conference on Neural Information Processing Systems, NeurIPS 2018

作者： Zhang, Linfeng Han, Jiequn Wang, Han Saidi, Wissam A. Car, Roberto Weinan, E. Program in Applied and Computational Mathematics Princeton University United States Institute of Applied Physics and Computational Mathematics China CAEP Software Center for High Performance Numerical Simulation China Department of Mechanical Engineering and Materials Science University of Pittsburgh United States Department of Chemistry Department of Physics Princeton University United States Princeton Institute for the Science and Technology of Materials Princeton University United States Department of Mathematics Princeton University United States Beijing Institute of Big Data Research China

Machine learning models are changing the paradigm of molecular modeling, which is a fundamental tool for material science, chemistry, and computational biology. Of particular interest is the inter-atomic potential energy surface (PES). Here we develop Deep Potential - Smooth Edition (DeepPot-SE), an end-to-end machine learning-based PES model, which is able to efficiently represent the PES of a wide variety of systems with the accuracy of ab initio quantum mechanics models. By construction, DeepPot-SE is extensive and continuously differentiable, scales linearly with system size, and preserves all the natural symmetries of the system. Further, we show that DeepPot-SE describes finite and extended systems including organic molecules, metals, semiconductors, and insulators with high fidelity. © 2018 Curran Associates Inc..All rights reserved.

关键词： Potential energy

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Author Correction: Contribution of Ryugu-like material to Earth’s volatile inventory by Cu and Zn isotopic analysis

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Nature Astronomy 2023年 633页

作者： Marine Paquet Frederic Moynier Wei Dai Yan Hu Martin Bizzarro Marc Chaussidon Tetsuya Yokoyama Ikshu Gautam Makiko K. Haba Akira Ishikawa Yuki Masuda Yoshinari Abe Jérôme Aléon Conel M. O’D. Alexander Richard W. Carlson Larry Nittler Sachiko Amari Yuri Amelin Ken-ichi Bajo Noriyuki Kawasaki Sohei Wada Hisayoshi Yurimoto Audrey Bouvier Byeon-Gak Choi Nicolas Dauphas Andrew M. Davis Tommaso Di Rocco Andreas Pack Wataru Fujiya Ryota Fukai Tomohiro Usui Kanako Sakamoto Masanao Abe Akiko Miyazaki Aiko Nakato Masahiro Nishimura Tatsuaki Okada Toru Yada Kasumi Yogata Satoru Nakazawa Takanao Saiki Satoshi Tanaka Yuichi Tsuda Makoto Yoshikawa Yuki Hibiya Hiroshi Hidaka Sei-ichiro Watanabe Hisashi Homma Peter Hoppe Gary R. Huss Alexander N. Krot Kazuhide Nagashima Kiyohiro Ichida Shintaro Komatani Mayu Morita Morihiko Onose Tsuyoshi Iizuka Trevor R. Ireland Motoo Ito Takaaki Noguchi Shoichi Itoh Noriko T. Kita Kouki Kitajima Thorsten Kleine Ming-Chang Liu Kevin D. McKeegan Lauren Tafla Haolan Tang Edward D. Young Kazuko Motomura Izumi Nakai David Nesvorný Ann N. Nguyen Changkun Park Laurette Piani Liping Qin Sara S. Russell Naoya Sakamoto Maria Schönbächler Kentaro Terada Yasuko Terada Meenakshi Wadhwa Richard J. Walker Katsuyuki Yamashita Qing-Zhu Yin Shigekazu Yoneda Hiroharu Yui Ai-Cheng Zhang Tomoki Nakamura Hiroshi Naraoka Ryuji Okazaki Hikaru Yabuta Fuyuto Terui Shogo Tachibana Université Paris Cité Institut de Physique du Globe de Paris CNRS Paris France Centre for Star and Planet Formation GLOBE Institute University of Copenhagen Copenhagen Denmark Department of Earth and Planetary Sciences Tokyo Institute of Technology Tokyo Japan Graduate School of Engineering Materials Science and Engineering Tokyo Denki University Tokyo Japan Institut de Minéralogie de Physique des Matériaux et de Cosmochimie Sorbonne Université Muséum National d’Histoire Naturelle CNRS UMR 7590 IRD Paris France Earth and Planets Laboratory Carnegie Institution for Science Washington DC USA McDonnell Center for the Space Sciences and Physics Department Washington University St. Louis MO USA Guangzhou Institute of Geochemistry Chinese Academy of Sciences Guangzhou China Natural History Sciences IIL Hokkaido University Sapporo Japan Bayerisches Geoinstitut Universität Bayreuth Bayreuth Germany Department of Earth Science Education Seoul National University Seoul Republic of Korea Department of the Geophysical Sciences and Enrico Fermi Institute The University of Chicago Chicago IL USA Faculty of Geosciences and Geography University of Göttingen Göttingen Germany Faculty of Science Ibaraki University Mito Japan ISAS/JSEC JAXA Sagamihara Japan General Systems Studies The University of Tokyo Tokyo Japan Earth and Planetary Sciences Nagoya University Nagoya Japan Osaka Application Laboratory SBUWDX Rigaku Corporation Osaka Japan Max Planck Institute for Chemistry Mainz Germany Hawai’i Institute of Geophysics and Planetology University of Hawai’i at Mānoa Honolulu HI USA Analytical Technology Horiba Techno Service Co. Ltd Kyoto Japan Earth and Planetary Science The University of Tokyo Tokyo Japan School of Earth and Environmental Sciences The University of Queensland St Lucia Queensland Australia Kochi Institute for Core Sample Research JAMSTEC Kochi Japan Earth and Planetary Sciences Kyoto University Kyoto Japan Geoscience Universit

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Modeling the vertical growth of van der Waals stacked 2D materials using the diffuse domain method

arXiv

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arXiv 2019年

作者： Guo, Zhenlin Price, Christopher Shenoy, Vivek B. Lowengrub, John Department of Mathematics University of California IrvineCA92697-3875 United States Department of Materials Science and Engineering University of Pennsylvania PhiladelphiaPA19104-6272 United States Department of Mechanical Engineering & Applied Mechanics University ofPennsylvania PhiladelphiaPA19104-6272 United States Bioengineering University of Pennsylvania PhiladelphiaPA19104-6272 United States Department of Biomedical Engineering University of California IrvineCA92697-3875 United States

Vertically-stacked monolayers of graphene and other atomically-thin 2D materials have attracted considerable research interest because of their potential in fabricating materials with specifically-designed properties. Chemical vapor deposition has proved to be an efficient and scalable fabrication method. However, a lack of mechanistic understanding has hampered efforts to control the fabrication process beyond empirical trial-and-error approaches. In this paper, we develop a general multiscale Burton-Cabrera-Frank (BCF) type model of the vertical growth of 2D materials to predict the necessary growth conditions for vertical versus in-plane (monolayer) growth of arbitrarily-shaped layers. This extends previous work where we developed such a model assuming the layers were fully-faceted (Ye et al., ACS Nano, 11, 12780-12788, 2017). To solve the model numerically, we reformulate the system using the phase-field/diffuse domain method that enables the equations to be solved in a fixed regular domain. We use a second-order accurate, adaptive finite-difference/nonlinear multigrid algorithm to discretize and solve the discrete system. We investigate the effect of parameters, including the van der Waals interaction energies between the layers, the kinetic attachment rates, the edge-energies and the deposition flux, on layer growth and morphologies. While the conditions that favor vertical growth generally follow an analytic thermodynamic criterion we derived for circular layers, the layer boundaries may develop significant curvature during growth, consistent with experimental observations. Our approach provides a mechanistic framework for controlling and optimizing the growth multilayered 2D materials. Copyright © 2019, The Authors. All rights reserved.

关键词： Transition metals

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Kramers nodal lines in intercalated TaS2 superconductors

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Nature Communications 2025年第1期16卷 1-10页

作者： Zhang, Yichen Gao, Yuxiang Pulkkinen, Aki Guo, Xingyao Huang, Jianwei Guo, Yucheng Yue, Ziqin Oh, Ji Seop Moon, Alex Oudah, Mohamed Gao, Xue-Jian Marmodoro, Alberto Fedorov, Alexei Mo, Sung-Kwan Hashimoto, Makoto Lu, Donghui Rajapitamahuni, Anil Vescovo, Elio Kono, Junichiro Hallas, Alannah M. Birgeneau, Robert J. Balicas, Luis Minár, Ján Hosur, Pavan Law, Kam Tuen Morosan, Emilia Yi, Ming Department of Physics and Astronomy Rice University Houston 77005 TX United States New Technologies Research Center University of West Bohemia Plzen 301 00 Czech Republic Department of Physics Hong Kong University of Science and Technology Clear Water Bay Hong Kong Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston 77005 TX United States Smalley-Curl Institute Rice University Houston 77005 TX United States Department of Physics University of California Berkeley Berkeley 94720 CA United States National High Magnetic Field Laboratory Tallahassee Tallahassee 32310 FL United States Physics Department Florida State University Tallahassee 32306 FL United States Stewart Blusson Quantum Matter Institute University of British Columbia Vancouver Vancouver V6T 1Z4 BC Canada Advanced Light Source Lawrence Berkeley National Laboratory Berkeley Berkeley 94720 CA United States Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park 94025 CA United States National Synchrotron Light Source II Brookhaven National Lab Upton 11973 NY United States Rice Center for Quantum Materials Rice University Houston 77005 TX United States Department of Electrical and Computer Engineering Rice University Houston 77005 TX United States Department of Materials Science and NanoEngineering Rice University Houston 77005 TX United States Department of Physics & Astronomy University of British Columbia Vancouver Vancouver V6T 1Z1 BC Canada Canadian Institute for Advanced Research Toronto Toronto M5G 1M1 ON Canada Materials Science Division Lawrence Berkeley National Laboratory Berkeley Berkeley 94720 CA United States Department of Physics and Texas Center for Superconductivity University of Houston Houston 77204 TX United States

Kramers degeneracy is one fundamental embodiment of the quantum mechanical nature of particles with half-integer spin under time reversal symmetry. Under the chiral and noncentrosymmetric achiral crystalline symmetries, Kramers degeneracy emerges respectively as topological quasiparticles of Weyl fermions and Kramers nodal lines (KNLs), anchoring the Berry phase-related physics of electrons. However, an experimental demonstration for ideal KNLs well isolated at the Fermi level is lacking. Here, we establish a class of noncentrosymmetric achiral intercalated transition metal dichalcogenide superconductors with large Ising-type spin-orbit coupling, represented by InxTaS2, to host an ideal KNL phase. We provide evidence from angle-resolved photoemission spectroscopy with spin resolution, angle-dependent quantum oscillation measurements, and ab-initio calculations. Our work not only provides a realistic platform for realizing and tuning KNLs in layered materials, but also paves the way for exploring the interplay between KNLs and superconductivity, as well as applications pertaining to spintronics, valleytronics, and nonlinear transport. © The Author(s) 2025.

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engineering chirality at wafer scale with ordered carbon nanotube architectures

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Nature communications 2023年第1期14卷 7380页

作者： Jacques Doumani Minhan Lou Oliver Dewey Nina Hong Jichao Fan Andrey Baydin Keshav Zahn Yohei Yomogida Kazuhiro Yanagi Matteo Pasquali Riichiro Saito Junichiro Kono Weilu Gao Department of Electrical and Computer Engineering Rice University Houston TX USA. Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston TX USA. Department of Electrical and Computer Engineering The University of Utah Salt Lake City UT USA. Carbon Hub Rice University Houston TX USA. Department of Chemical and Biomolecular Engineering Rice University Houston TX USA. J.A. Woollam Co. Inc. Lincoln NE USA. Smalley-Curl Institute Rice University Houston TX USA. Department of Physics Tokyo Metropolitan University Tokyo Japan. Department of Chemistry Rice University Houston TX USA. Department of Materials Science and NanoEngineering Rice University Houston TX USA. Department of Physics Tohoku University Sendai Japan. Department of Physics National Taiwan Normal University Taipei Taiwan. Department of Physics and Astronomy Rice University Houston TX USA. Department of Electrical and Computer Engineering The University of Utah Salt Lake City UT USA. weilu.gao@utah.edu. Carbon Hub Rice University Houston TX USA. weilu.gao@utah.edu.

Creating artificial matter with controllable chirality in a simple and scalable manner brings new opportunities to diverse areas. Here we show two such methods based on controlled vacuum filtration - twist stacking and mechanical rotation - for fabricating wafer-scale chiral architectures of ordered carbon nanotubes (CNTs) with tunable and large circular dichroism (CD). By controlling the stacking angle and handedness in the twist-stacking approach, we maximize the CD response and achieve a high deep-ultraviolet ellipticity of 40 ± 1 mdeg nm. Our theoretical simulations using the transfer matrix method reproduce the experimentally observed CD spectra and further predict that an optimized film of twist-stacked CNTs can exhibit an ellipticity as high as 150 mdeg nm, corresponding to a g factor of 0.22. Furthermore, the mechanical rotation method not only accelerates the fabrication of twisted structures but also produces both chiralities simultaneously in a single sample, in a single run, and in a controllable manner. The created wafer-scale objects represent an alternative type of synthetic chiral matter consisting of ordered quantum wires whose macroscopic properties are governed by nanoscopic electronic signatures and can be used to explore chiral phenomena and develop chiral photonic and optoelectronic devices.

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Using physical features of protein core packing to distinguish real proteins from decoys

arXiv

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arXiv 2020年

作者： Grigas, Alex T. Mei, Zhe Treado, John D. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute signifficantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (speciffically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features. Copyright © 2020, The Authors. All rights reserved.

关键词： Proteins

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Grain boundary shear coupling is not a grain boundary property

arXiv

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arXiv 2018年

作者： Chen, Kongtao Han, Jian Thomas, Spencer L. Srolovitz, David J. Department of Materials Science and Engineering University of Pennsylvania PhiladelphiaPA19104 United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania PhiladelphiaPA19104 United States Department of Materials Science and Engineering City University of Hong Kong Hong Kong

Shear coupling implies that all grain boundary (GB) migration necessarily creates mechanical stresses/strains and is a key component to the evolution of all polycrystalline microstructures. We present MD simulation data and theoretical analyses that demonstrate the GB shear coupling is not an intrinsic GB property, but rather strongly depends on the type and magnitude of the driving force for migration and temperature. We resolve this apparent paradox by proposing a microscopic theory for GB migration that is based upon a statistical ensemble of line defects (disconnections) that are constrained to lie in the GB. Comparison with the MD results for several GBs provides quantitative validation of the theory as a function of stress, chemical potential jump and temperature. Copyright © 2018, The Authors. All rights reserved.

关键词： Grain boundaries

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Grain Growth and Solid-State Dewetting of Bi-Crystal Ni-Fe Thin Films on Sapphire

SSRN

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SSRN 2018年

作者： Sharma, Amit Kumar, Aakash Gazit, Nimrod Srolovitz, David J. Rabkin, Eugen Department of Materials Science and Engineering Israel Institute of Technology Haifa32000 Israel Department of Materials Science and Engineering University of Pennsylvania PhiladelphiaPA19004 United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania PhiladelphiaPA19004 United States Department of Materials Science and Engineering City University of Hong Kong Kowloon Hong Kong

We studied the solid-state dewetting behavior of thin Ni80Fe20 films deposited on basal plane oriented sapphire substrate and annealed in the range of temperatures of 1023-1323 K. All studied films exhibited strong texture and maze bicrystal microstructure, with only two grains misoriented by 60° around the common axis present in the film. The morphology of partially dewetted films changed from the one typical for polycrystalline thin films to the one typical for single crystalline heteroepitaxial films with increasing temperatures and annealing times. This change of dewetting behavior was associated with the fast grain growth in the films. The films of pure Ni of identical thickness, annealed under identical conditions exhibited significantly slower grain growth and lower thermal stability. Both the high-resolution X-ray diffraction and the cross-sectional high-resolution transmission electron microscopy observations revealed the phase separation of the Ni80Fe20 films into two parallel layers of the face-centered cubic (adjacent to the substrate) and hexagonal close-packed (on the top of the film) phases of similar compositions. Our density functional theory (DFT) calculations indicated that this phase separation is driven by the decrease of the film surface and interface energy, leading to the thermodynamically equilibrium thickness of the metastable hexagonal close-packed phase. This phase exhibits higher surface anisotropy than its stable face-centered cubic counterpart and is instrumental in accelerating the grain growth in the film via suppression of grain boundary grooving. © 2018, The Authors. All rights reserved.

关键词： Thin films

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