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arXiv 2022年

作者： Aubry, Jean-Francois Bates, Oscar Boehm, Christian Pauly, Kim Butts Christensen, Douglas Cueto, Carlos Gélat, Pierre Guasch, Lluis Jaros, Jiri Jing, Yun Jones, Rebecca Li, Ningrui Marty, Patrick Montanaro, Hazael Neufeld, Esra Pichardo, Samuel Pinton, Gianmarco Pulkkinen, Aki Stanziola, Antonio Thielscher, Axel Treeby, Bradley Van't Wout, Elwin Physics for Medicine Paris INSERM U1273 ESPCI Paris PSL University CNRS UMR 8063 France Department of Bioengineering Imperial College London Exhibition Road LondonSW7 2AZ United Kingdom Institute of Geophysics ETH Zürich Sonneggstrasse 5 Zürich8092 Switzerland Department of Radiology Stanford University StanfordCA United States Department of Biomedical Engineering Department of Electrical and Computer Engineering University of Utah United States Department of Surgical Biotechnology Division of Surgery and Interventional Science University College London LondonNW3 2PF United Kingdom Earth Science and Engineering Department Imperial College London London United Kingdom Centre of Excellence IT4Innovations Faculty of Information Technology Brno University of Technology Bozetechova 2 Brno612 00 Czech Republic Graduate Program in Acoustics The Pennsylvania State University University Park PA16802 United States Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill North Carolina State University NC United States Department of Electrical Engineering Stanford University StanfordCA United States Zurich Switzerland Laboratory for Acoustics / Noise control Empa Swiss Federal Laboratories for Materials Science and Technology Dubendorf Switzerland Zurich Switzerland Radiology and Clinical Neurosciences Departments Cumming School of Medicine University of Calgary Canada Department of Applied Physics University of Eastern Finland Kuopio70211 Finland Department of Medical Physics and Biomedical Engineering University College London Gower Street LondonWC1E 6BT United Kingdom Technical University of Denmark Denmark Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre Denmark Institute for Mathematical and Computational Engineering School of Engineering and Faculty of Mathematics Pontificia Universidad Catolica de Chile Santiago Chile

computational models of acoustic wave propagation are frequently used in transcranial ultrasound therapy, for example, to calculate the intracranial pressure field or to calculate phase delays to correct for skull distortions. To allow intercomparison between the different modeling tools and techniques used by the community, an international working group was convened to formulate a set of numerical benchmarks. Here, these benchmarks are presented, along with intercomparison results. Nine different benchmarks of increasing geometric complexity are defined. These include a single-layer planar bone immersed in water, a multi-layer bone, and a whole skull. Two transducer configurations are considered (a focused bowl and a plane piston), giving a total of 18 permutations of the benchmarks. Eleven different modeling tools are used to compute the benchmark results. The models span a wide range of numerical techniques, including the finite-difference time-domain method, angular-spectrum method, pseudospectral method, boundary-element method, and spectral-element method. Good agreement is found between the models, particularly for the position, size, and magnitude of the acoustic focus within the skull. When comparing results for each model with every other model in a cross comparison, the median values for each benchmark for the difference in focal pressure and position are less than 10% and 1 mm, respectively. The benchmark definitions, model results, and intercomparison codes are freely available to facilitate further comparisons. Copyright © 2022, The Authors. All rights reserved.

关键词： Bone

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The Athena++ adaptive mesh refinement framework: Design and magnetohydrodynamic solvers

arXiv

引用

arXiv 2020年

作者： Stone, James M. Tomida, Kengo White, Christopher J. Felker, Kyle G. Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Earth and Space Science Osaka University Toyonaka Osaka560-0043 Japan Kavli Institute for Theoretical Physics University of California Santa Barbara Santa BarbaraCA93107 United States School of Natural Sciences Institute for Advanced Study PrincetonNJ08544 United States Astronomical Institute Tohoku University Sendai Miyagi980-8578 Japan Argonne National Laboratory LemontIL60439 United States

The design and implementation of a new framework for adaptive mesh refinement (AMR) calculations is described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use for a wide variety of physics. The framework works with both uniform and nonuniform grids in Cartesian and curvilinear coordinate systems. It adopts a dynamic execution model based on a simple design called a "task list" that improves parallel performance by overlapping communication and computation, simplifies the inclusion of a diverse range of physics, and even enables multiphysics models involving different physics in different regions of the calculation. We describe physics modules implemented in this framework for both non-relativistic and relativistic magnetohydrodynamics (MHD). These modules adopt mature and robust algorithms originally developed for the Athena MHD code and incorporate new extensions: support for curvilinear coordinates, higher-order time integrators, more realistic physics such as a general equation of state, and diffusion terms that can be integrated with super-time-stepping algorithms. The modules show excellent performance and scaling, with well over 80% parallel efficiency on over half a million threads. The source code has been made publicly available. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetohydrodynamics

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2022 Review of Data-Driven Plasma science

arXiv

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arXiv 2022年

作者： Anirudh, Rushil Archibald, Rick Asif, M. Salman Becker, Markus M. Benkadda, Sadruddin Bremer, Peer-Timo Budé, Rick H.S. Chang, C.S. Chen, Lei Churchill, R.M. Citrin, Jonathan Gaffney, Jim A. Gainaru, Ana Gekelman, Walter Gibbs, Tom Hamaguchi, Satoshi Hill, Christian Humbird, Kelli Jalas, Sören Kawaguchi, Satoru Kim, Gon-Ho Kirchen, Manuel Klasky, Scott Kline, John L. Krushelnick, Karl Kustowski, Bogdan Lapenta, Giovanni Li, Wenting Ma, Tammy Mason, Nigel J. Mesbah, Ali Michoski, Craig Munson, Todd Murakami, Izumi Najm, Habib N. Erik J. Olofsson, K. Park, Seolhye Peterson, J. Luc Probst, Michael Pugmire, David Sammuli, Brian Sawlani, Kapil Scheinker, Alexander Schissel, David P. Shalloo, Rob J. Shinagawa, Jun Seong, Jaegu Spears, Brian K. Tennyson, Jonathan Thiagarajan, Jayaraman Ticoş, Catalin M. Trieschmann, Jan van Dijk, Jan Van Essen, Brian Ventzek, Peter Wang, Haimin Wang, Jason T.L. Wang, Zhehui Wende, Kristian Xu, Xueqiao Yamada, Hiroshi Yokoyama, Tatsuya Zhang, Xinhua Lawrence Livermore National Laboratory LivermoreCA94550 United States Oak Ridge National Laboratory Oak RidgeTN37830 United States University of California Riverside RiversideCA92521 United States Felix-Hausdorff-Str. 2 Greifswald17489 Germany Aix Marseille University CNRS PIIM UMR 7345 Marseille France Department of Applied Physics Eindhoven University of Technology Netherlands Princeton Plasma Physics Laboratory Princeton NJ08540 United States Institute of Ion Physics and Applied Physics University of Innsbruck Technikerstrasse 25 Innsbruck6020 Austria DIFFER - Dutch Institute for Fundamental Energy Research Eindhoven Netherlands Science and Technology of Nuclear Fusion Group Eindhoven University of Technology Eindhoven Netherlands Department of Physics and Astronomy University of California Los AngelesCA90095 United States NVIDIA 2788 San Tomas Expressway Santa ClaraCA95051 United States Center for Atomic and Molecular Technologies Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita Osaka Japan Department of Nuclear Sciences and Applications International Atomic Energy Agency Wagramer Strasse 5 PO Box 100 Vienna1400 Austria Center for Free-Electron Laser Science Department of Physics Universität Hamburg Luruper Chaussee 149 Hamburg22761 Germany Division of Information and Electronic Engineering Graduate School of Engineering Muroran Institute of Technology Hokkaido Muroran050-8585 Japan Seoul National University Seoul151-741 Korea Republic of Deutsches Elektronen-Synchrotron DESY Notkestr. 85 Hamburg22607 Germany Los Alamos National Laboratory Los AlamosNM87545 United States Center for Ultrafast Optical Science University of Michigan Ann ArborMI48109-2099 United States Department of Mathematics KULeuven University of Leuven Belgium Department of Physical Sciences The University of Kent CanterburyCT2 7NH United Kingdom Department of Chemical and Biomolecular Engineering University of California Berk

Data science and technology offer transformative tools and methods to science. This review article highlights latest development and progress in the interdisciplinary field of data-driven plasma science (DDPS). A large amount of data and machine learning algorithms go hand in hand. Most plasma data, whether experimental, observational or computational, are generated or collected by machines today. It is now becoming impractical for humans to analyze all the data manually. Therefore, it is imperative to train machines to analyze and interpret (eventually) such data as intelligently as humans but far more efficiently in quantity. Despite the recent impressive progress in applications of data science to plasma science and technology, the emerging field of DDPS is still in its infancy. Fueled by some of the most challenging problems such as fusion energy, plasma-processing of materials, and fundamental understanding of the universe through observable plasma phenomena, it is expected that DDPS continues to benefit significantly from the interdisciplinary marriage between plasma science and data science into the foreseeable future. Copyright © 2022, The Authors. All rights reserved.

关键词： Machine learning

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Unsupervised particle sorting for high-resolution single-particle cryo-EM

arXiv

引用

arXiv 2019年

作者： Zhou, Ye Moscovich, Amit Bendory, Tamir Bartesaghi, Alberto Department of Computer Science Duke University Durham United States Program in Applied and Computational Mathematics Princeton University United States School of Electrical Engineering Tel Aviv University Tel Aviv Israel Department of Biochemistry Duke University School of Medicine Durham United States Department of Electrical and Computer Engineering Duke University Durham United States

Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and data processing, have significantly lowered the barrier for non-expert users to successfully execute the structure determination workflow. Many critical data processing steps, however, still require expert user intervention in order to converge to the correct high-resolution structure. In particular, strategies to identify homogeneous populations of particles rely heavily on subjective criteria that are not always consistent or reproducible among different users. Here, we explore the use of unsupervised strategies for particle sorting that are compatible with the autonomous operation of the image processing pipeline. More specifically, we show that particles can be successfully sorted based on a simple statistical model for the distribution of scores assigned during refinement. This represents an important step towards the development of automated workflows for protein structure determination using single-particle *** Codes 62P10 Copyright © 2019, The Authors. All rights reserved.

关键词： Inverse problems

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Ellipticity-dependent sequential over-barrier ionization of cold rubidium

arXiv

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arXiv 2020年

作者： Yuan, Junyang Liu, Shiwei Wang, Xincheng Shen, Zhenjie Ma, Yixuan Ma, Huanyu Meng, Qiuxiang Yan, Tian-Min Zhang, Yizhu Dorn, Alexander Weidemüller, Matthias Ye, Difa Jiang, Yuhai Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai201210 China University of Chinese Academy of Sciences Beijing100049 China School of Physical Science and Technology ShanghaiTech University Shanghai201210 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China Graduate School China Academy of Engineering Physics Beijing100193 China Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering Key Laboratory of Optoelectronics Information and Technical Science Ministry of Education Tianjin University Tianjin300072 China Max-Planck-Institut für Kernphysik Saupfercheckweg 1 HeidelbergDE-69117 Germany Hefei National Laboratory for Physical Sciences at the Microscale and Shanghai Branch University of Science and Technology of China Shanghai201315 China CAS Center for Excellence Synergetic Innovation Center in Quantum Information and Quantum Physics University of Science and Technology of China Shanghai201315 China Physikalisches Institut Universität Heidelberg Im Neuenheimer Feld 226 Heidelberg69120 Germany

We perform high-resolution measurements of momentum distribution on Rbn+ recoil ions up to charge state n = 4, where laser-cooled rubidium atoms are ionized by femtosecond elliptically polarized lasers with the pulse duration of 35 fs and the intensity of 3.3×1015 W/cm2 in the over-barrier ionization (OBI) regime. The momentum distributions of the recoil ions are found to exhibit multi-band structures as the ellipticity varies from the linear to circular polarizations. The origin of these band structures can be explained quantitatively by the classical OBI model and dedicated classical trajectory Monte Carlo simulations with Heisenberg potential. Specifically, with back analysis of the classical trajectories, we reveal the ionization time and the OBI geometry of the sequentially released electrons, disentangling the mechanisms behind the tilted angle of the band structures. These results indicate that the classical treatment can describe the strong-field multiple ionization processes of alkali atoms. Copyright © 2020, The Authors. All rights reserved.

关键词： Monte Carlo methods

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TWO-SAMPLE TEST OF COMMUNITY MEMBERSHIPS OF WEIGHTED STOCHASTIC BLOCK MODELS

arXiv

引用

arXiv 2018年

作者： Li, Yezheng Li, Hongzhe Program in Applied Mathematics and Computational Science University of Pennsylvania PhiladelphiaPA19104 United States University of Pennsylvania PhiladelphiaPA19104 United States

Suppose two networks are observed for the same set of nodes, where each network is assumed to be generated from a weighted stochastic block model. This paper considers the problem of testing whether the community memberships of the two networks are the same. A test statistic based on singular subspace distance is developed. Under the weighted stochastic block models with dense graphs, the limiting distribution of the proposed test statistic is developed. Simulation results show that the test has correct empirical type 1 errors under the dense graphs. The test also behaves as expected in empirical power, showing gradual changes when the intra-block and inter-block distributions are close and achieving 1 when the two distributions are not so close, where the closeness of the two distributions is characterized by Renyi divergence of order 1/2. The Enron email networks are used to demonstrate the proposed *** Codes 62E20, 62F03, 62H15, 91D30, 62F05 Copyright © 2018, The Authors. All rights reserved.

关键词： Clustering algorithms

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Hard convex lens-shaped particles: Characterization of dense disordered packings

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Physical Review E 2019年第6期100卷 062902-062902页

作者： Giorgio Cinacchi Salvatore Torquato Departamento de Física Teórica de la Materia Condensada Instituto de Física de la Materia Condensada (IFIMAC) Instituto de Ciencias de Materiales “Nicolás Cabrera” Universidad Autónoma de Madrid Ciudad Universitaria de Cantoblanco E-28049 Madrid Spain Department of Chemistry and Department of Physics Institute for the Science and Technology of Materials Program for Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Among the family of hard convex lens-shaped particles (lenses), the one with aspect ratio equal to 2/3 is “optimal” in the sense that the maximally random jammed (MRJ) packings of such lenses achieve the highest packing fraction ϕMRJ≃0.73 [G. Cinacchi and S. Torquato, Soft Matter 14, 8205 (2018)]. This value is only a few percent lower than ϕDKP=0.76210⋯, the packing fraction of the corresponding densest-known crystalline (degenerate) packings [G. Cinacchi and S. Torquato, J. Chem. Phys. 143, 224506 (2015)]. By exploiting the appreciably reduced propensity that a system of such optimal lenses has to positionally and orientationally order, disordered packings of them are progressively generated by a Monte Carlo method–based procedure from the dilute equilibrium isotropic fluid phase to the dense nonequilibrium MRJ state. This allows us to closely monitor how the (micro)structure of these packings changes in the process of formation of the MRJ state. The gradual changes undergone by the many structural descriptors calculated here can coherently and consistently be traced back to the gradual increase in contacts between the hard particles until the isostatic mean value of ten contact neighbors per lens is reached at the effectively hyperuniform MRJ state. Compared to the MRJ state of hard spheres, the MRJ state of such optimal lenses is denser (less porous), more disordered, and rattler-free. This set of characteristics makes them good glass formers. It is possible that this conclusion may also hold for other hard convex uniaxial particles with a correspondingly similar aspect ratio, be they oblate or prolate, and that, by using suitable biaxial variants of them, that set of characteristics might further improve.

关键词： Granular packing Jamming Colloids Disordered systems Granular materials Lyotropic liquid crystals Monte Carlo methods

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

arXiv

引用

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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Hyperuniform states of matter

arXiv

引用

arXiv 2018年

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

Hyperuniform states of matter are correlated systems that are characterized by an anomalous suppression of long-wavelength (i.e., large-length-scale) density fluctuations compared to those found in garden-variety disordered systems, such as ordinary fluids and amorphous solids. All perfect crystals, perfect quasicrystals and special disordered systems are hyperuniform. Thus, the hyperuniformity concept enables a unified framework to classify and structurally characterize crystals, quasicrystals and the exotic disordered varieties. While disordered hyperuniform systems were largely unknown in the scientific community over a decade ago, now there is a realization that such systems arise in a host of contexts across the physical, materials, chemical, mathematical, engineering, and biological sciences, including disordered ground states, glass formation, jamming, Coulomb systems, spin systems, photonic and electronic band structure, localization of waves and excitations, self-organization, fluid dynamics, number theory, stochastic point processes, integral and stochastic geometry, the immune system, and photoreceptor cells. Such unusual amorphous states can be obtained via equilibrium or nonequilibrium routes, and come in both quantum-mechanical and classical varieties. The connections of hyperuniform states of matter to many different areas of fundamental science appear to be profound and yet our theoretical understanding of these unusual systems is only in its infancy. The purpose of this review article is to introduce the reader to the theoretical foundations of hyperuniform ordered and disordered systems. Special focus will be placed on fundamental and practical aspects of the disordered kinds, including our current state of knowledge of these exotic amorphous systems as well as their formation and novel physical properties. Copyright © 2018, The Authors. All rights reserved.

关键词： Ground state

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Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

引用

Physical Review Letters 2018年第14期120卷 143001-143001页

作者： Linfeng Zhang Jiequn Han Han Wang Roberto Car Weinan E Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA and Center for Data Science Beijing International Center for Mathematical Research Peking University Beijing Institute of Big Data Research Beijing 100871 People’s Republic of China

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

关键词： Classical statistical mechanics Density functional theory First-principles calculations Interatomic & molecular potentials Learning Neuronal networks Potential energy surfaces Solid-state chemistry Thermal properties Van der Waals interaction Molecular dynamics

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