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Corrigendum to: A more accurate three-dimensional grain growth algorithm [Acta Mater. 59 (2011) 6837–6847]

Acta Materialia 2014年 71卷 390-390页

作者： Emanuel A. Lazar Jeremy K. Mason Robert D. MacPherson David J. Srolovitz Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA School of Mathematics Institute for Advanced Study Princeton NJ 08540 USA IHPC 1 Fusionopolis Way 16-16 Connexis Singapore 138632 Singapore

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Cross-system biological image quality enhancement based on the generative adversarial network as a foundation for establishing a multi-institute microscopy cooperative network

arXiv

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arXiv 2024年

作者： Panek, Dominik Rząca, Carina Szczypior, Maksymilian Sorysz, Joanna Misztal, Krzysztof Baster, Zbigniew Rajfur, Zenon Doctoral School of Exact and Natural Sciences Jagiellonian University ul. Lojasiewicza 11 Kraków30-348 Poland Department of Molecular and Interfacial Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate Program in Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate program in Biomedical Engineering Faculty of Electrical Engineering Automatics Computer Science and Biomedical Engineering AGH University of Science and Technology Al. A. Mickiewicza 30 Building B-1 Kraków30-059 Poland Division of Computational Mathematics Faculty of Mathematics and Computer Science Jagiellonian University 6 Lojasiewicza St. Kraków Poland

High-quality fluorescence imaging of biological systems is limited by processes like photobleaching and phototoxicity, and also in many cases, by limited access to the latest generations of microscopes. Moreover, low temporal resolution can lead to a motion blur effect in living systems. Our work presents a deep learning (DL) generative-adversarial approach to the problem of obtaining high-quality (HQ) images based on their low-quality (LQ) equivalents. We propose a generative-adversarial network (GAN) for contrast transfer between two different separate microscopy systems: a confocal microscope (producing HQ images) and a wide-field fluorescence microscope (producing LQ images). Our model proves that such transfer is possible, allowing us to receive HQ-generated images characterized by low mean squared error (MSE) values, high structural similarity index (SSIM), and high peak signal-to-noise ratio (PSNR) values. For our best model in the case of comparing HQ-generated images and HQ-ground truth images, the median values of the metrics are 6·10-4, 0.9413, and 31.87, for MSE, SSIM, and PSNR, respectively. In contrast, in the case of comparison between LQ and HQ ground truth median values of the metrics are equal to 0.0071, 0.8304, and 21.48 for MSE, SSIM, and PSNR respectively. Therefore, we observe a significant increase ranging from 14% to 49% for SSIM and PSNR respectively. These results, together with other single-system cross-modality studies, provide proof of concept for further implementation of a cross-system biological image quality enhancement. © 2024, CC BY-SA.

关键词： Fluorescence imaging

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Nonlinear Geometric Effects in Mechanical Bistable Morphing Structures

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Physical Review Letters 2012年第11期109卷 114302-114302页

作者： Zi Chen Qiaohang Guo Carmel Majidi Wenzhe Chen David J. Srolovitz Mikko P. Haataja Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials (PRISM) Princeton University Princeton New Jersey 08544 USA Department of Biomedical Engineering Washington University St. Louis Missouri 63130 USA College of Materials Science and Engineering Fuzhou University Fuzhou Fujian 350108 China Department of Mathematics and Physics Fujian University of Technology Fuzhou Fujian 350108 China Department of Mechanical Engineering Carnegie Mellon University Pittsburgh Pennsylvania 15213 USA Department of Materials Science and Engineering Fujian University of Technology Fuzhou Fujian 350108 China Institute for High Performance Computing 1 Fusionopolis Way Singapore 138632 Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA School of Mathematics Institute for Advanced Study Princeton New Jersey 08540 USA

Bistable structures associated with nonlinear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeling such large deformation behavior of shells, the roles of mechanical and nonlinear geometric effects on bistability remain elusive. We demonstrate, through both theoretical analysis and tabletop experiments, that two dimensionless parameters control bistability. Our work classifies the conditions for bistability, and extends the large deformation theory of plates and shells.

关键词： NONLINEAR theories DEFORMATIONS (Mechanics) PARAMETER estimation OPTICAL bistability STRUCTURAL shells PLATES (Engineering) CRYSTAL structure

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Parameter inference with non-linear galaxy clustering: accounting for theoretical uncertainties

arXiv

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arXiv 2021年

作者： Knabenhans, Mischa Brinckmann, Thejs Stadel, Joachim Schneider, Aurel Teyssier, Romain Institute for Computational Science University of Zurich Winterthurerstrasse 190 Zurich8057 Switzerland Dipartimento di Fisica Scienze della Terra Universitá degli Studi di Ferrara via Giuseppe Saragat 1 Ferrara44122 Italy Sezione di Ferrara Via Giuseppe Saragat 1 Ferrara44122 Italy C.N. Yang Institute for Theoretical Physics Department of Physics & Astronomy Stony Brook University Stony BrookNY11794 United States Department of Astrophysical Sciences Princeton University 4 Ivy Lane PrincetonNJ08544 United States The Program in Applied and Computational Mathematics Princeton University Fine Hall Washington Road PrincetonNJ08544-1000 United States

We implement EuclidEmulator (version 1), an emulator for the non-linear correction of the matter power spectrum, into the Markov chain Monte Carlo (MCMC) forecasting code MontePython. We compare the performance of HALOFIT, HMCode, and EuclidEmulator1, both at the level of power spectrum prediction and at the level of posterior probability distributions of the cosmological parameters, for different cosmological models and different galaxy power spectrum wave number cutoffs. We confirm that the choice of the power spectrum predictor has a non-negligible effect on the computed sensitivities when doing cosmological parameter forecasting, even for a conservative wave number cut-off of 0.2 ℎMpc−1. We find that EuclidEmulator1 is on average up to 17% more sensitive to the cosmological parameters than the other two codes, with the most significant improvements being for the Hubble parameter of up to 42% and the equation of state of dark energy of up to 26%, depending on the case. In addition, we point out that the choice of the power spectrum predictor contributes to the risk of computing a significantly biased mean cosmology when doing parameter estimations. For the four tested scenarios we find biases, averaged over the cosmological parameters, of between 0.5 and 2σ (from below 1σ up to 6σ for individual parameters). This paper provides a proof of concept that this risk can be mitigated by taking a well-tailored theoretical uncertainty into account as this allows to reduce the bias by a factor of 2 to 5, depending on the case under consideration, while keeping posterior credibility contours small: the standard deviations are amplified by a factor of ≤ 1.4 in all cases. © 2021, CC BY-NC-SA.

关键词： Power spectrum

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The Disordered Heterogeneous Universe: Galaxy Distribution and Clustering Across Length Scales

arXiv

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arXiv 2022年

作者： Philcox, Oliver H.E. Torquato, Salvatore Department of Astrophysical Sciences Princeton University PrincetonNJ08540 United States School of Natural Sciences Institute for Advanced Study 1 Einstein Drive PrincetonNJ08540 United States Center for Theoretical Physics Department of Physics Columbia University New YorkNY10027 United States Simons Foundation New YorkNY10010 United States Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States

The studies of disordered heterogeneous media and galaxy cosmology share a common goal: analyzing the disordered distribution of particles and/or building blocks at ‘microscales’ to predict physical properties of the medium at ‘macroscales’, whether it be a liquid, colloidal suspension, composite material, galaxy cluster, or entire Universe. The theory of disordered heterogeneous media provides an array of theoretical and computational techniques to characterize a wide class of complex material microstructures. In this work, we apply them to describe the disordered distributions of galaxies obtained from recent suites of dark matter simulations. We focus on the determination of lower-order correlation functions, ‘void’ and ‘particle’ nearest-neighbor functions, certain cluster statistics, pair-connectedness functions, percolation properties, and a scalar order metric to quantify the degree of order. Compared to analogous homogeneous Poisson and typical disordered systems, the cosmological simulations exhibit enhanced large-scale clustering and longer tails in the void and particle nearest-neighbor functions, due to the presence of quasi-long-range correlations imprinted by early Universe physics, with a minimum particle separation far below the mean nearest-neighbor distance. On large scales, the system appears ‘hyperuniform’, as a result of primordial density fluctuations, whilst on the smallest scales, the system becomes almost ‘antihyperuniform’, as evidenced by its number variance. Additionally, via a finite scaling analysis, we compute the percolation threshold of the galaxy catalogs, finding this to be significantly lower than for Poisson realizations (at reduced density ηc = 0.25 in our fiducial analysis compared to ηc = 0.34), with strong dependence on the mean density;this is consistent with the observation that the galaxy distribution contains voids of up to 50% larger radius. However, the two sets of simulations appear to share the same fractal dimension

关键词： Galaxies

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25th Annual computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

引用

BMC NEUROSCIENCE 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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Erratum: “Effect of dimensionality on the continuum percolation of overlapping hyperspheres and hypercubes. II. Simulation results and analyses” [J. Chem. Phys. 137, 074106 (2012)]

引用

The Journal of Chemical Physics 2014年第15期141卷

作者： S. Torquato Y. Jiao 1Department of Chemistry Department of Physics Princeton Center for Theoretical Science and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA 2Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

In Table I and the caption of Fig. 8 of Ref. 1, the numerical value of the percolation threshold ηc of three-dimensional overlapping spheres as determined via t

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26th Annual computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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Towards Implementation of the Pressure-Regulated, Feedback-Modulated Model of Star Formation in Cosmological Simulations: Methods and Application to TNG

arXiv

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arXiv 2024年

作者： Hassan, Sultan Ostriker, Eve C. Kim, Chang-Goo Bryan, Greg L. Burger, Jan D. Fielding, Drummond B. Forbes, John C. Genel, Shy Hernquist, Lars Jeffreson, Sarah M.R. Motwani, Bhawna Smith, Matthew C. Somerville, Rachel S. Steinwandel, Ulrich P. Teyssier, Romain Center for Cosmology and Particle Physics Department of Physics New York University 726 Broadway New YorkNY10003 United States Center for Computational Astrophysics Flatiron Institute 162 5th Ave New YorkNY10010 United States Department of Physics & Astronomy University of the Western Cape Cape Town7535 South Africa Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Institute for Advanced Study 1 Einstein Drive PrincetonNJ08540 United States Department of Astronomy Columbia University 550 W 120th Street New YorkNY10027 United States Max-Planck-Institut für Astrophysik Karl-Schwarzschild-Str. 1 GarchingD-85748 Germany Department of Astronomy Cornell University IthacaNY14853 United States School of Physical and Chemical Sciences-Te Kura Matū University of Canterbury Private Bag 4800 Christchurch8140 New Zealand Columbia Astrophysics Laboratory Columbia University 550 West 120th Street New YorkNY10027 United States Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA United States Program in Applied and Computational Mathematics Princeton University Fine Hall Washington Road PrincetonNJ08544-1000 United States

Traditional star formation subgrid models implemented in cosmological galaxy formation simulations, such as that of Springel & Hernquist (2003, hereafter SH03), employ adjustable parameters to satisfy constraints measured in the local Universe. In recent years, however, theory and spatially-resolved simulations of the turbulent, multiphase, star-forming ISM have begun to produce new first-principles models, which when fully developed can replace traditional subgrid prescriptions. This approach has advantages of being physically motivated and predictive rather than empirically tuned, and allowing for varying environmental conditions rather than being tied to local Universe conditions. As a prototype of this new approach, by combining calibrations from the TIGRESS numerical framework with the Pressure-Regulated Feedback-Modulated (PRFM) theory, simple formulae can be obtained for both the gas depletion time and an effective equation of state. Considering galaxies in TNG50, we compare the "native" simulation outputs with post-processed predictions from PRFM. At TNG50 resolution, the total midplane pressure is nearly equal to the total ISM weight, indicating that galaxies in TNG50 are close to satisfying vertical equilibrium. The measured gas scale height is also close to theoretical equilibrium predictions. The slopes of the effective equations of states are similar, but with effective velocity dispersion normalization from SH03 slightly larger than that from current TIGRESS simulations. Because of this and the decrease in PRFM feedback yield at high pressure, the PRFM model predicts shorter gas depletion times than the SH03 model at high densities and redshift. Our results represent a first step towards implementing new, numerically calibrated subgrid algorithms in cosmological galaxy formation simulations. Copyright © 2024, The Authors. All rights reserved.

关键词： Cosmology

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

arXiv

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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

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