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High-speed and low-power molecular dynamics processing unit(MDPU)with ab initio accuracy

npj computational Materials 2024年第1期10卷 559-568页

作者： Pinghui Mo Yujia Zhang Zhuoying Zhao Hanhan Sun Junhua Li Dawei Guan Xi Ding Xin Zhang Bo Chen Mengchao Shi Duo Zhang Denghui Lu Yinan Wang Jianxing Huang Fei Liu Xinyu Li Mohan Chen Jun Cheng Bin Liang Weinan E Jiayu Dai Linfeng Zhang Han Wang Jie Liu College of Integrated Circuits Hunan UniversityChangsha410082P.R.China College of Electrical and Information Engineering Hunan UniversityChangsha410082P.R.China College of Computer National University of Defense TechnologyChangsha410073P.R.China Department of Physics National University of Defense TechnologyChangsha410073P.R.China DP Technology 100080 BeijingP.R.China AI for Science Institute 100080 BeijingP.R.China Academy for Advanced Interdisciplinary Studies Peking University100871 BeijingP.R.China HEDPS CAPTCollege of EngineeringPeking University100871 BeijingP.R.China School of Mathematical Science Peking University100871 BeijingP.R.China State Key Laboratory of Physical Chemistry of Solid Surfaces iChEMCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamen361005P.R.China School of Integrated Circuits Peking University100871 BeijingP.R.China Center for Machine Learning Research Peking University100871 BeijingP.R.China Institute of Applied Physics and Computational Mathematics 100088 BeijingP.R.China Greater Bay Area Institute for Innovation Hunan UniversityGuangzhou511300P.R.China Department of Electrical and Computer Engineering University of WashingtonSeattleWA98195USA

Molecular dynamics(MD)is an indispensable atomistic-scale computational tool widely-used in various *** the past decades,nearly all ab initio MD and machine-learning MD have been based on the general-purpose central/graphics processing units(CPU/GPU),which are well-known to suffer from their intrinsic“memory wall”and“power wall”***,nowadays MD calculations with ab initio accuracy are extremely time-consuming and power-consuming,imposing serious restrictions on the MD simulation size and *** solve this problem,here we propose a special-purpose MD processing unit(MDPU),which could reduce MD time and power consumption by about 103 times(109 times)compared to state-of-the-art machine-learningMD(ab initio MD)based on CPU/GPU,while keeping ab initio *** significantly-enhanced performance,the proposed MDPU may pave a way for the accurate atomistic-scale analysis of large-size and/or longduration problems which were impossible/impractical to compute before.

关键词： consuming power MDP

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Fabrication and bioactivity studies of wollastonite/polycaprolactone composites

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International Journal of Nano and Biomaterials 2023年第2期10卷 86-99页

作者： Lakshmi, R. Choudhary, Rajan Senatov, Fedor Kaloshkin, Sergey Kothandam, Shobana Ponnamma, Deepalekshmi Sadasivuni, Kishor Kumar Swamiappan, Sasikumar Department of Chemistry Auxilium College Tamil Nadu Vellore632006 India Faculty of Materials Science and Applied Chemistry Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU Institute of General Chemical Engineering Riga Technical University Pulka St 3 RigaLV-1007 Latvia Baltic Biomaterials Centre of Excellence Headquarters at Riga Technical University Kipsala Street 6A RigaLV-1048 Latvia National University of Science and Technology "MISiS" Moscow119049 Russia Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Tamil Nadu Vellore632014 India Materials Science and Technology Program Department of Mathematics Statistics and Physics College of Arts and Sciences Qatar University P.O. Box 2713 Doha Qatar Center for Advanced Materials Qatar University P.O. Box 2713 Doha Qatar Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Tamil Nadu Vellore632014 India

Current work investigates the influence of wollastonite on mechanical stability and biomineralisation ability of wollastonite/ polycaprolactone (PCL) composites (WP composites). The solvent casting particulate leaching method was used to prepare these composites. FT-IR spectra indicated the presence of functional groups associated with PCL and wollastonite. Scanning electron microscopy showed aggregated morphology and wollastonite particles were embedded in the PCL matrix. The incorporation of wollastonite leads to a more than three-fold increase in the compressive strength of the composites. Moreover, the composites containing 50% wollastonite exhibited better compressive strength than 80%. This observation suggested that if the concentration of a filler is exceeded beyond its critical concentration then the mechanical stability of the composite will be compromised. The composites revealed good apatite deposition ability. Thus, the biomineralisation ability and compressive strength of PCL can be improved by preparing its composites with bioceramics. © 2023 Inderscience Enterprises Ltd.

关键词： Bioceramics

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Wellposedness and scattering for the generalized Boussinesq equation

arXiv

引用

arXiv 2021年

作者： Chen, Jie Guo, Boling Shao, Jie Institute of Applied Physics and Computational Mathematics Beijing100088 China Department of Mathematics Nanjing University of Science and Technology Nanjing210094 China School of Mathematical Sciences Peking University Beijing100871 China

In this paper, we show the local well-posedness of the generalized Boussinesq equation(gBQ) in L2(Rd),H1(Rd) and obtain the global well-posedness, finite-time blowup and small initial data scattering of gBQ in energy space H1(Rd). Moreover, we obtain the large radial initial data scattering of defocusing case for d ≥ 3 by using the method of Dodson-Murphy. © 2021, CC BY.

关键词： Partial differential equations

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CONVERGENCE OF THE PLANEWAVE APPROXIMATIONS FOR QUANTUM INCOMMENSURATE SYSTEMS

arXiv

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arXiv 2022年

作者： Wang, Ting Chen, Huajie Zhou, Aihui Zhou, Yuzhi Massatt, Daniel School of Mathematical Sciences Beijing Normal University Beijing100875 China LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China School of Mathematical Sciences University of Chinese Academy of Sciences Beijing100049 China CAEP Software Center for High Performance Numerical Simulation Beijing100088 China Institute of Applied Physics and Computational Mathematics Beijing100094 China Mathematics Department Louisiana State University LA70802 United States

Incommensurate structures come from stacking the single layers of low-dimensional materials on top of one another with misalignment such as a twist in orientation. While these structures are of significant physical interest, they pose many theoretical challenges due to the loss of periodicity. This paper studies the physical observables of continuum Schrödinger operators for incommensurate systems. We characterize the density of states and local density of states in real and reciprocal spaces, and develop novel numerical methods to approximate them. In particular, we (i) justify the thermodynamic limit of the density of states and local density of states via the operator kernel characterization;and (ii) propose efficient numerical schemes based on planewave approximation and trapezoidal rule in reciprocal space. We present both rigorous analysis and numerical simulations to support the reliability and efficiency of our numerical *** Codes 65Z05, 81-08, 47G30 Copyright © 2022, The Authors. All rights reserved.

关键词： Numerical methods

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computational Characterization of the Recently Synthesized Pristine and Porous 12-Atom-Wide Armchair Graphene Nanoribbon

arXiv

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arXiv 2025年

作者： da Gomes, Djardiel S. Felix, Isaac M. Radel, Willian F. Dias, Alexandre C. Ribeiro Junior, Luiz A. Pereira Junior, Marcelo L. State University of Campinas Gleb Wataghin Institute of Physics Department of Applied Physics Campinas São Paulo13083-859 Brazil University of Brasília Faculty UnB Planaltina Materials Science Postgraduate Program Federal District Brasília Brazil Center for Agri-food Science and Technology Federal University of Campina Grande Paraíba Pombal58840-000 Brazil University of Brasília Institute of Physics Physics Postgraduate Program Federal District Brasília70910900 Brazil Institute of Physics International Center of Physics University of Brasília Federal District Brasília70910-900 Brazil Institute of Physics University of Brasília Federal District Brasília70910-900 Brazil Computational Materials Laboratory University of Brasília Federal District Brasília70910900 Brazil University of Brasília College of Technology Department of Electrical Engineering Federal District Brasília70910-900 Brazil

Recently synthesized Porous 12-Atom-Wide Armchair Graphene Nanoribbons (12-AGNRs) [Nano Lett. 2024, 24, 10718-10723]exhibit tunable properties through periodic porosity, enabling precise control over their electronic, optical, thermal, and mechanical behavior. This work presents a comprehensive theoretical characterization of pristine and porous 12-AGNRs based on density functional theory (DFT) and molecular dynamics (MD) simulations. DFT calculations reveal substantial electronic modifications, including band gap widening and the emergence of localized states. Analyzed within the Bethe–Salpeter equation (BSE) framework, optical properties highlight strong excitonic effects and significant absorption shifts. Thermal transport simulations indicate a pronounced reduction in conductivity due to enhanced phonon scattering at nanopores. At the same time, MD-based mechanical analysis shows decreased stiffness and strength while maintaining structural integrity. Despite these modifications, porous 12-AGNRs remain mechanically and thermally stable. These findings establish porosity engineering as a powerful strategy for tailoring graphene nanoribbons’ functional properties, reinforcing their potential for nanoelectronic, optoelectronic, and thermal management *** Codes 00-xx © 2025, CC BY.

关键词： Nanoribbons

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On the unimportance of memory for the time non-local components of the Kadanoff-Baym equations

arXiv

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arXiv 2023年

作者： Reeves, Cian C. Zhu, Yuanran Yang, Chao Vlček, Vojtěch Department of Physics University of California Santa Barbara Santa BarbaraCA93117 United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Chemistry and Biochemistry University of California Santa Barbara Santa BarbaraCA93117 United States Department of Materials University of California Santa Barbara Santa BarbaraCA93117 United States

The generalized Kadanoff-Baym ansatz (GKBA) is an approximation to the Kadanoff-Baym equations (KBE), that neglects certain memory effects that contribute to the Green’s function at non-equal times. Here we present arguments and numerical results to demonstrate the practical insignificance of the quantities neglected when deriving the GKBA at conditions at which KBE and GKBA are appropriate. We provide a mathematical proof that places a scaling bound on the neglected terms, further reinforcing that these terms are typically small in comparison to terms that are kept in the GKBA. We perform calculations in a range of models, including different system sizes and filling fractions, as well as experimentally relevant non-equilibrium excitations. We find that both the GKBA and KBE capture the dynamics of interacting systems with moderate and even strong interactions well. We explicitly compute terms neglected in the GKBA approximation and show, in the scenarios tested here, that they are orders of magnitude smaller than the terms that are accounted for, i.e., they offer only a small correction when included in the full Kadanoff-Baym equations. © 2023, CC BY.

关键词： Dynamics

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Optimization of transformer ratio and beam loading in a plasma wakefield accelerator with a structure-exploiting algorithm

arXiv

引用

arXiv 2023年

作者： Su, Q. Larson, J. Dalichaouch, T.N. Li, F. An, W. Hildebrand, L. Zhao, Y. Decyk, V. Alves, P. Wild, S.M. Mori, W.B. Department of Electrical and Computer Engineering University of California Los Angeles Los AngelesCA90095 United States Mathematics and Computer Science Division Argonne National Laboratory LemontIL60439 United States Department of Physics and Astronomy University of California Los Angeles Los AngelesCA90095 United States Department of Astronomy Beijing Normal University Beijing100875 China Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

Plasma-based acceleration has emerged as a promising candidate as an accelerator technology for a future linear collider or a next-generation light source. We consider the plasma wakefield accelerator (PWFA) concept where a plasma wave wake is excited by a particle beam and a trailing beam surfs on the wake. For a linear collider, the energy transfer efficiency from the drive beam to the wake and from the wake to the trailing beam must be large, while the emittance and energy spread of the trailing bunch must be preserved. One way to simultaneously achieve this when accelerating electrons is to use longitudinally shaped bunches and nonlinear wakes. In the linear regime, there is an analytical formalism to obtain the optimal shapes. In the nonlinear regime, however, the optimal shape of the driver to maximize the energy transfer efficiency cannot be precisely obtained because currently no theory describes the wake structure and excitation process for all degrees of nonlinearity. In addition, the ion channel radius is not well defined at the front of the wake where the plasma electrons are not fully blown out by the drive beam. We present results using a novel optimization method to effectively determine a current profile for the drive and trailing beam in PWFA that provides low energy spread, low emittance, and high acceleration efficiency. We parameterize the longitudinal beam current profile as a piecewise-linear function and define optimization objectives. For the trailing beam, the algorithm converges quickly to a nearly inverse trapezoidal trailing beam current profile similar to that predicted by the ultrarelativistic limit of the nonlinear wakefield theory. For the drive beam, the beam profile found by the optimization in the nonlinear regime that maximizes the transformer ratio also resembles that predicted by linear theory. The current profiles found from the optimization method provide higher transformer ratios compared with the linear ramp predicted by the

关键词： Energy transfer

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Local Number Fluctuations in Hyperuniform and Nonhyperuniform Systems: Higher-Order Moments and Distribution Functions

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Physical Review X 2021年第2期11卷 021028-021028页

作者： Salvatore Torquato Jaeuk Kim Michael A. Klatt Department of Physics Princeton University Princeton New Jersey 08544 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 Institut für Theoretische Physik FAU Erlangen-Nürnberg Staudtstr. 7 91058 Erlangen Germany

The local number variance σ2(R) associated with a spherical sampling window of radius R enables a classification of many-particle systems in d-dimensional Euclidean space Rd according to the degree to which large-scale density fluctuations are suppressed, resulting in a demarcation between hyperuniform and nonhyperuniform phyla. To more completely characterize density fluctuations, we carry out an extensive study of higher-order moments or cumulants, including the skewness γ1(R), excess kurtosis γ2(R), and the corresponding probability distribution function P[N(R)] of a large family of models across the first three space dimensions, including both hyperuniform and nonhyperuniform systems with varying degrees of short- and long-range order. To carry out this comprehensive program, we derive new theoretical results that apply to general point processes, and we conduct high-precision numerical studies. Specifically, we derive explicit closed-form integral expressions for γ1(R) and γ2(R) that encode structural information up to three-body and four-body correlation functions, respectively. We also derive rigorous bounds on γ1(R), γ2(R), and P[N(R)] for general point processes and corresponding exact results for general packings of identical spheres. High-quality simulation data for γ1(R), γ2(R), and P[N(R)] are generated for each model. We also ascertain the proximity of P[N(R)] to the normal distribution via a novel Gaussian “distance” metric l2(R). Among all models, the convergence to a central limit theorem (CLT) is generally fastest for the disordered hyperuniform processes in two or higher dimensions such that γ1(R)∼l2(R)∼R−(d+1)/2 and γ2(R)∼R−(d+1) for large R. The convergence to a CLT is slower for standard nonhyperuniform models and slowest for the “antihyperuniform” model studied here. We prove that one-dimensional hyperuniform systems of class I or any d-dimensional lattice cannot obey a CLT. Remarkably, we discover a type of universality in that, for all of ou

关键词： Exotic phases of matter Fluctuations & noise Nonequilibrium statistical mechanics Surface & interfacial phenomena

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Gap Sensitivity Reveals Universal Behaviors in Optimized Photonic Crystal and Disordered Networks

引用

Physical Review Letters 2021年第3期127卷 037401-037401页

作者： Michael A. Klatt Paul J. Steinhardt Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Institut für Theoretische Physik University of Erlangen-Nürnberg Staudtstr. 7 91058 Erlangen Germany Department of Chemistry Princeton Institute for the Science and Technology of Materialsand Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

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)≡dΔ(α)/dα, the first derivative of the optimal gap-to-midgap ratio Δ(α). In particular, for all our crystal networks, S(α) takes a universal form that is well approximated by the analytic formula for a 1D 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 heterostructures.

关键词： Photonic crystals Diamond structure Networks & random structures Random & disordered media Band structure methods

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Dynamic Measure of Hyperuniformity and Nonhyperuniformity in Heterogeneous Media via the Diffusion Spreadability

arXiv

引用

arXiv 2021年

作者： Wang, Haina Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Princeton Center for Theoretical Science Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Time-dependent interphase diffusion processes in multiphase heterogeneous media arise ubiquitously in physics, chemistry and biology. Examples of heterogeneous media include composites, geological media, gels, foams and cell aggregates. The recently developed concept of spreadability, S(t), provides a direct link between time-dependent diffusive transport and the microstructure of two-phase media across length scales [Torquato, S., Phys. Rev. E., 104 054102 (2021)]. To investigate the capability of S(t) to probe microstructures of real heterogeneous media, we explicitly compute S(t) for well-known two-dimensional and three-dimensional idealized model structures that span across nonhyperuniform and hyperuniform classes. Among the former class, we study fully penetrable spheres and equilibrium hard spheres, and in the latter class, we examine sphere packings derived from "perfect glasses", uniformly randomized lattices (URL), disordered stealthy hyperuniform point processes and Bravais lattices. Hyperuniform media are characterized by an anomalous suppression of volume fraction fluctuations at large length scales compared to that of any nonhyperuniform medium. We further confirm that the small-, intermediate- and long-time behaviors of S(t) sensitively capture the small-, intermediate- and large-scale characteristics of the models. In instances in which the spectral density (Equation presented)V (k) has a power-law form B|k|α in the limit |k| → 0, the long-time spreadability provides a simple means to extract the value of the coefficients α and B that is robust against noise in (Equation presented)V (k) at small wavenumbers. For typical nonhyperuniform media, the intermediate-time spreadability is slower for models with larger values of the coefficient B = (Equation presented)V (0). Interestingly, the excess spreadability S(∞) - S(t) for URL packings has nearly exponential decay at small to intermediate t, but transforms to a power-law decay at large t, and the time f

关键词： Diffusion

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