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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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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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Structural Properties of Hyperuniform Networks

arXiv

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arXiv 2024年

作者： Newby, Eli Shi, Wenlong Jiao, Yang Albert, Reka Torquato, Salvatore Department of Physics Pennsylvania State University University ParkPA16802 United States Materials Science and Engineering Arizona State University TempeAZ85287 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Disordered hyperuniform many-particle systems are recently discovered exotic states of matter, characterized by a complete suppression of normalized infinite-wavelength density fluctuations, as in perfect crystals, and lack of conventional long-range order, as in liquids and glasses. In this work, we begin a program to quantify the structural properties of nonhyperuniform and hyperuniform networks. In particular, large two-dimensional (2D) Voronoi networks (graphs) containing approximately 10,000 nodes are created from a variety of different point configurations, including the antihyperuniform hyperplane intersection process (HIP), nonhyperuniform Poisson process, nonhyperuniform random sequential addition (RSA) saturated packing, and both non-stealthy and stealthy hyperuniform point processes. We carry out an extensive study of the Voronoi-cell area distribution of each of the networks through determining multiple metrics that characterize the distribution, including their higher-cumulants (i.e., skewness 1 and excess kurtosis 2). We show that the HIP distribution is far from Gaussian, as evidenced by a high skewness (γ1 = 3.16) and large positive excess kurtosis (γ2 = 16.2). The Poisson (with γ1 = 1.07 and γ2 = 1.79) and non-stealthy hyperuniform (with γ1 = 0.257 and γ2 = 0.0217) distributions are Gaussian-like distributions, since they exhibit a small but positive skewness and excess kurtosis. The RSA (with γ1 = 0.450 and γ2 = -0.0384) and the highest stealthy hyperuniform distributions (with γ1 = 0.0272 and γ2 = -0.0626) are also non-Gaussian because of their low skewness and negative excess kurtosis, which is diametrically opposite non-Gaussian behavior of the HIP. The fact that the cell-area distributions of large, finite-sized RSA and stealthy hyperuniform networks (e.g., with N ≈ 10, 000 nodes) are narrower, have larger peaks, and smaller tails than a Gaussian distribution implies that in the thermodynamic limit the distributions should exhibit compact suppo

关键词： Gaussian distribution

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Lithospheric foundering and underthrusting imaged beneath Tibet

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Nature Communications 2017年第1期8卷 1-10页

作者： Chen, Min Niu, Fenglin Tromp, Jeroen Lenardic, Adrian Lee, Cin-Ty A. Cao, Wenrong Ribeiro, Julia 318 Keith-Wiess Geology Lab Department of Earth Science Rice University 6100 Main Street Houston 77005 TX United States State Key Laboratory of Petroleum Resource Prospecting and Unconventional Natural Gas Institute China University of Petroleum Beijing 102249 China Department of Geosciences Princeton University Princeton 08544 NJ United States Program in Applied and Computational Mathematics Princeton University Princeton 08544 NJ United States

Long-standing debates exist over the timing and mechanism of uplift of the Tibetan Plateau and, more specifically, over the connection between lithospheric evolution and surface expressions of plateau uplift and volcanism. Here we show a T-shaped high wave speed structure in our new tomographic model beneath South-Central Tibet, interpreted as an upper-mantle remnant from earlier lithospheric foundering. Its spatial correlation with ultrapotassic and adakitic magmatism supports the hypothesis of convective removal of thickened Tibetan lithosphere causing major uplift of Southern Tibet during the Oligocene. Lithospheric foundering induces an asthenospheric drag force, which drives continued underthrusting of the Indian continental lithosphere and shortening and thickening of the Northern Tibetan lithosphere. Surface uplift of Northern Tibet is subject to more recent asthenospheric upwelling and thermal erosion of thickened lithosphere, which is spatially consistent with recent potassic volcanism and an imaged narrow low wave speed zone in the uppermost mantle. © 2017 The Author(s).

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Corrigendum:‘‘Reconnection of two vortex rings’’ [Phys. Fluids A 1, 630 (1989)]

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Physics of Fluids A: Fluid Dynamics 1990年第4期2卷 638-638页

作者： S. Kida M. Takaoka F. Hussain Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 Department of Physics Faculty of Science Kyoto University Kyoto 606 Japan Department of Mechanical Engineering University of Houston Houston Texas 77004

S. Kida, M. Takaoka, F. Hussain; Corrigendum:‘‘Reconnection of two vortex rings’’ [Phys. Fluids A 1, 630 (1989)]Comments, Physics of Fluids A: Fluid Dynamics, V

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Simulating Cardiac Fluid Dynamics in the Human Heart

arXiv

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arXiv 2023年

作者： Davey, Marshall Puelz, Charles Rossi, Simone Smith, Margaret Anne Wells, David R. Sturgeon, Gregory M. Segars, W. Paul Vavalle, John P. Peskin, Charles S. Griffith, Boyce E. University of North Carolina Chapel HillNC United States Department of Pediatrics-Cardiology Baylor College of Medicine Texas Children’s Hospital HoustonTX United States Department of Mathematics University North Carolina Chapel HillNC United States Department of Radiology Duke University Medical Center DurhamNC United States Division of Cardiology Department of Medicine University of North Carolina School of Medicine Chapel HillNC United States Courant Institute of Mathematical Sciences New York University New YorkNY United States Departments of Mathematics and Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina School of Medicine Chapel HillNC United States McAllister Heart Institute University of North Carolina School of Medicine Chapel HillNC United States

Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin, flexible valve leaflets. There has been longstanding scientific, engineering, and medical interest in creating mathematical models of the heart that capture, explain, and predict these fluid-structure interactions. However, existing computational models that account for interactions among the blood, the actively contracting myocardium, and the cardiac valves are limited in their abilities to predict valve performance, resolve fine-scale flow features, or use realistic descriptions of tissue biomechanics. Here we introduce and benchmark a comprehensive mathematical model of cardiac fluid dynamics in the human heart. A unique feature of our model is that it incorporates biomechanically detailed descriptions of all major cardiac structures that are calibrated using tensile tests of human tissue specimens to reflect the heart’s microstructure. Further, it is the first fluid-structure interaction model of the heart that provides anatomically and physiologically detailed representations of all four cardiac valves. We demonstrate that this integrative model generates physiologic dynamics, including realistic pressure-volume loops that automatically capture isovolumetric contraction and relaxation, and predicts fine-scale flow features. None of these outputs are prescribed;instead, they emerge from interactions within our comprehensive description of cardiac physiology. Such models can serve as tools for predicting the impacts of medical devices or clinical interventions. They also can serve as platforms for mechanistic studies of cardiac pathophysiology and dysfunction, including congenital defects, cardiomyopathies, and heart failure, that are difficult or impossible to perform in patients. Copyright © 2023, The Authors. All rights reserved.

关键词： Heart

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computational Design of Anisotropic Stealthy Hyperuniform Composites with Engineered Directional Scattering Properties

arXiv

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arXiv 2023年

作者： Shi, Wenlong Keeney, David Chen, Duyu Jiao, Yang Torquato, Salvatore Materials Science and Engineering Arizona State University TempeAZ85287 United States Materials Research Laboratory University of California Santa BarbaraCA93106 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Disordered hyperuniform materials are an emerging class of exotic amorphous states of matter that endow them with singular physical properties, including large isotropic photonic band gaps, superior resistance to fracture, and nearly optimal electrical and thermal transport properties, to name but a few. Here, we generalize the Fourier-space based numerical construction procedure for designing and generating digital realizations of isotropic disordered hyperuniform two-phase heterogeneous materials (i.e., composites) developed by Chen and Torquato [Acta Mater. 142, 152 (2018)] to anisotropic microstructures with targeted spectral densities. Our generalized construction procedure explicitly incorporates the vector-dependent spectral density function χ˜V (k) of arbitrary form that is realizable. We demonstrate the utility of the procedure by generating a wide spectrum of anisotropic stealthy hyperuniform (SHU) microstructures with χ˜V (k) = 0 for k ∈ Ω, i.e., complete suppression of scattering in an "exclusion" region Ω around the origin in the Fourier space. We show how different exclusion-region shapes with various discrete symmetries, including circular-disk, elliptical-disk, square, rectangular, butterfly-shaped and lemniscate-shaped regions of varying size, affect the resulting statistically anisotropic microstructures as a function of the and phase volume fraction. The latter two cases of Ω lead to directionally hyperuniform composites, which are stealthy hyperuniform only along certain directions, and are non-hyperuniform along others. We find that, while the circular-disk exclusion regions give rise to isotropic hyperuniform composite microstructures, the directional hyperuniform behaviors imposed by the shape asymmetry (or anisotropy) of certain exclusion regions give rise to distinct anisotropic structures and degree of uniformity in the distribution of the phases on intermediate and large length scales along different directions. Moreover, while the anisotr

关键词： Volume fraction

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Algebraic constraints and algorithms for common lines in cryo-EM

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Biological imaging 2024年 4卷 e9页

作者： Tommi Muller Adriana L Duncan Eric J Verbeke Joe Kileel Mathematical Institute University of Oxford Oxford UK. Department of Mathematics University of Texas at Austin Austin TX USA. Program in Applied and Computational Mathematics Princeton University Princeton NJ USA. Oden Institute University of Texas at Austin Austin TX USA.

We revisit the topic of common lines between projection images in single-particle cryo-electron microscopy (cryo-EM). We derive a novel low-rank constraint on a certain 2 × matrix storing properly scaled basis vectors for the common lines between projection images of one molecular conformation. Using this algebraic constraint and others, we give optimization algorithms to denoise common lines and recover the unknown 3D rotations associated with the images. As an application, we develop a clustering algorithm to partition a set of noisy images into homogeneous communities using common lines, in the case of discrete heterogeneity in cryo-EM. We demonstrate the methods on synthetic and experimental datasets.

关键词： ADMM common lines cryo-electron microscopy discrete heterogeneity group synchronization low-rank matrix

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Publisher's Note: “Reacting and non-reacting, three-dimensional shear layers with spanwise stretching” [Phys. Fluids 34, 123602 (2022)]

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Physics of Fluids 2023年第1期35卷

作者： Jonathan L. Palafoutas William A. Sirignano 1Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08540 USA 2Department of Mechanical and Aerospace Engineering University of California Irvine Irvine California 92697 USA

This article was published online on 2 December 2022 with errors throughout the paper. All the derivative terms had the wrong denominator; the denominators were

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Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function (vol 571, pg 403, 2019)

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NATURE 2019年第7773期573卷 E2-E2页

作者： Bailis, Will Shyer, Justin A. Zhao, Jun Canaveras, Juan Carlos Garcia Al Khazal, Fatimah J. Qu, Rihao Steach, Holly R. Bielecki, Piotr Khan, Omair Jackson, Ruaidhri Kluger, Yuval Maher, Louis J., III Rabinowitz, Joshua Craft, Joe Flavell, Richard A. Department of Immunobiology Yale School of Medicine New Haven USA Department of Pathology Children’s Hospital of Philadelphia Philadelphia USA Department of Pathology Yale School of Medicine New Haven USA Program of Computational Biology and Bioinformatics Yale University New Haven USA Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton USA Department of Chemistry Princeton University Princeton USA Diabetes Research Center University of Pennsylvania Philadelphia USA Department of Biochemistry and Molecular Biology Mayo Clinic College of Medicine and Science Rochester USA Applied Mathematics Program Yale University New Haven USA Department of Internal Medicine (Rheumatology) Yale School of Medicine New Haven USA Howard Hughes Medical Institute Chevy Chase USA

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

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