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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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Moduli spaces and breather dynamics of analytic solutions in chiral magnets without Heisenberg exchange interaction

arXiv

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arXiv 2024年

作者： Barton-Singer, Bruno Bolognesi, Stefano Gudnason, Sven Bjarke Menta, Roberto Institute of Applied and Computational Mathematics Foundation for Research and Technology - Hellas Heraklion700 13 Greece Department of Physics "E. Fermi" University of Pisa INFN Sezione di Pisa Largo Pontecorvo 3 Ed. C Pisa56127 Italy Institute of Contemporary Mathematics School of Mathematics and Statistics Henan University Henan Kaifeng475004 China Scuola Normale Superiore Piazza dei Cavalieri 7 Laboratorio NEST Piazza S. Silvestro 12 Pisa56127 Italy

We investigate the special case of the chiral magnet with vanishing Heisenberg exchange energy, whose axisymmetric Skyrmion solution has previously been found. The dynamical equations of this model look like inviscid fluid flow, and by investigating path-lines of this flow we can construct explicit static and dynamic solutions. We find an infinite-dimensional family of static Skyrmions that are related to the axisymmetric Skyrmion by co-ordinate transformations thus discovering a new moduli space, and further infinite-dimensional families of axisymmetric and non-axisymmetric breather-like supercompactons. We call the maps generating such moduli space "contour-preserving" maps. Copyright © 2024, The Authors. All rights reserved.

关键词： Exchange interactions

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Sachdev-Ye-Kitaev charging advantage as a random walk on graphs

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Physical Review B 2025年第7期111卷 075138-075138页

作者： Francisco Divi Jeff Murugan Dario Rosa ICTP South American Institute for Fundamental Research Instituto de Física Teórica UNESP - Universidade Estadual Paulista Rua Dr. Bento Teobaldo Ferraz 271 01140-070 São Paulo SP Brazil Perimeter Institute for Theoretical Physics Waterloo Ontario N2L 2Y5 Canada The Laboratory for Quantum Gravity & Strings Department of Mathematics and Applied Mathematics University of Cape Town Cape Town South Africa The National Institute for Theoretical and Computational Sciences Private Bag X1 Matieland South Africa

We investigate the charging dynamics of Sachdev-Ye-Kitaev (SYK) models as quantum batteries, highlighting their capacity to achieve quantum charging advantages. By analytically deriving the scaling of the charging power in SYK batteries, we identify the two key mechanisms underlying this advantage: the use of operators scaling extensively with system size N and the facilitation of operator delocalization by specific graph structures. A graph-theoretic framework is introduced in which the charging process is recast as a random walk on a graph, enabling a quantitative analysis of operator spreading. Our results establish rigorous conditions for the quantum advantage in SYK batteries and extend these insights to graph-based SYK models, revealing broader implications for energy storage and quantum dynamics. This work opens avenues for leveraging quantum chaos and complex network structures in optimizing energy transfer processes.

关键词： Quantum chaos

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Optimized Large Hyperuniform Binary Colloidal Suspensions in Two Dimensions

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Physical Review Letters 2020年第6期125卷 068002-068002页

作者： Zheng Ma Enrique Lomba Salvatore Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

The creation of disordered hyperuniform materials with extraordinary optical properties (e.g., large complete photonic band gaps) requires a capacity to synthesize large samples that are effectively hyperuniform down to the nanoscale. Motivated by this challenge, we propose a feasible equilibrium fabrication protocol using binary paramagnetic colloidal particles confined in a 2D plane. The strong and long-ranged dipolar interaction induced by a tunable magnetic field is free from screening effects that attenuate long-ranged electrostatic interactions in charged colloidal systems. Specifically, we numerically find a family of optimal size ratios that makes the two-phase system effectively hyperuniform. We show that hyperuniformity is a general consequence of low isothermal compressibilities, which makes our protocol suitable to treat more general systems with other long-ranged interactions, dimensionalities, and/or polydispersity. Our methodology paves the way to synthesize large photonic hyperuniform materials that function in the visible to infrared range and hence may accelerate the discovery of novel photonic materials.

关键词： Applications of soft matter Colloids Disordered systems

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Deep neural network for the dielectric response of insulators

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Physical Review B 2020年第4期102卷 041121(R)-041121(R)页

作者： Linfeng Zhang Mohan Chen Xifan Wu Han Wang Weinan E Roberto Car Department of Chemistry Department of Physics Program in Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

We introduce a deep neural network to model in a symmetry preserving way the environmental dependence of the centers of the electronic charge. The model learns from ab initio density functional theory, wherein the electronic centers are uniquely assigned by the maximally localized Wannier functions. When combined with the deep potential model of the atomic potential energy surface, the scheme predicts the dielectric response of insulators for trajectories inaccessible to direct ab initio simulation. The scheme is nonperturbative and can capture the response of a mutating chemical environment. We demonstrate the approach by calculating the infrared spectra of liquid water at standard conditions, and of ice under extreme pressure, when it transforms from a molecular to an ionic crystal.

关键词： Electric polarization Electrical properties Electronic structure Ferroelectrics Liquids Piezoelectrics Density functional theory First-principles calculations Machine learning Molecular dynamics Multiscale modeling Wannier function methods

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Generation and structural characterization of Debye random media

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Physical Review E 2020年第4期102卷 043310-043310页

作者： Zheng Ma Salvatore Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

In their seminal paper on scattering by an inhomogeneous solid, Debye and coworkers proposed a simple exponentially decaying function for the two-point correlation function of an idealized class of two-phase random media. Such Debye random media, which have been shown to be realizable, are singularly distinct from all other models of two-phase media in that they are entirely defined by their one- and two-point correlation functions. To our knowledge, there has been no determination of other microstructural descriptors of Debye random media. In this paper, we generate Debye random media in two dimensions using an accelerated Yeong-Torquato construction algorithm. We then ascertain microstructural descriptors of the constructed media, including their surface correlation functions, pore-size distributions, lineal-path function, and chord-length probability density function. Accurate semianalytic and empirical formulas for these descriptors are devised. We compare our results for Debye random media to those of other popular models (overlapping disks and equilibrium hard disks) and find that the former model possesses a wider spectrum of hole sizes, including a substantial fraction of large holes. Our algorithm can be applied to generate other models defined by their two-point correlation functions, and their other microstructural descriptors can be determined and analyzed by the procedures laid out here.

关键词： Patterns in complex systems

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One-sided GRP solver and numerical boundary conditions for compressible fluid flows

arXiv

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arXiv 2021年

作者： Li, Jiequan Zhang, Qinglong Institute of Applied Physics and Computational Mathematics Beijing Center for Applied Physics and Technology Peking University China State Key Laboratory for Turbulence Research and Complex System Peking University China Department of Mathematics and Statistics Ningbo University China

In the computation of compressible fluid flows, numerical boundary conditions are always necessary for all physical variables at computational boundaries while just partial physical variables are often prescribed as physical boundary conditions. Certain extrapolation technique or ghost cells are often employed traditionally for this issue but spurious wave reflections often arise to cause numerical instability. In this paper, we associate this issue with the one-sided generalized Riemann problem (GRP) solver motivated by the accelerated piston problem in gas dynamics so that the extrapolation technique can be actually avoided. In fact, the compatibility arguments naturally requires to formulate the one-sided generalized Riemann problem and incorporate it into the numerical procedure of boundary conditions. As far as the interaction of nonlinear waves with physical boundaries, such a one-sided GRP solver shows significant effects, as numerical experiments demonstrate, on avoiding spurious wave reflections at the computational boundaries. Copyright © 2021, The Authors. All rights reserved.

关键词： Boundary conditions

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On the approximability of random-hypergraph MAX-3-XORSAT problems with quantum algorithms

arXiv

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arXiv 2023年

作者： Kapit, Eliot Barton, Brandon A. Feeney, Sean Grattan, George Patnaik, Pratik Sagal, Jacob Carr, Lincoln D. Oganesyan, Vadim Department of Physics Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Quantum Engineering Program Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Physics and Astronomy College of Staten Island CUNY Staten IslandNY10314 United States Physics Program and Initiative for the Theoretical Sciences The Graduate Center CUNY New YorkNY10016 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States

A canonical feature of the constraint satisfaction problems in NP is approximation hardness, where in the worst case, finding sufficient-quality approximate solutions is exponentially hard for all known methods. Fundamentally, the lack of any guided local minimum escape method ensures both exact and approximate classical approximation hardness, but the equivalent mechanism(s) for quantum algorithms are poorly understood. For algorithms based on Hamiltonian time evolution, we explore this question through the prototypically hard MAX-3-XORSAT problem class. We conclude that the mechanisms for quantum exact and approximation hardness are fundamentally distinct. We review known results from the literature, and identify mechanisms that make conventional quantum methods (such as Adiabatic Quantum Computing) weak approximation algorithms in the worst case. We construct a family of "spectrally filtered" quantum algorithms that escape these issues, and develop analytical theories for their performance. We show that, for random hypergraphs in the approximation-hard regime, if we define the energy to be E = Nunsat - Nsat, spectrally filtered quantum optimization will return states with E ≤ qmEGS (where EGS is the ground state energy) in sub-quadratic time, where conservatively, qm 0.59. This is in contrast to qm → 0 for the hardest instances with classical searches. We test all of these claims with extensive numerical simulations. We do not claim that this approximation guarantee holds for all possible hypergraphs, though our algorithm’s mechanism can likely generalize widely. These results suggest that quantum computers are more powerful for approximate optimization than had been previously assumed. © 2023, CC BY.

关键词： Constraint satisfaction problems

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Sequential Markov Chain Monte Carlo for Lagrangian Data Assimilation with Applications to Unknown Data Locations

arXiv

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arXiv 2023年

作者： Ruzayqat, Hamza Beskos, Alexandros Crisan, Dan Jasra, Ajay Kantas, Nikolas Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Statistical Science University College London LondonWC1E 6BT United Kingdom Department of Mathematics Imperial College London LondonSW7 2AZ United Kingdom

We consider a class of high-dimensional spatial filtering problems, where the spatial locations of observations are unknown and driven by the partially observed hidden signal. This problem is exceptionally challenging as not only is high-dimensional, but the model for the signal yields longer-range time dependencies through the observation locations. Motivated by this model we revisit a lesser-known and provably convergent computational methodology from [4, 11, 28] that uses sequential Markov Chain Monte Carlo (MCMC) chains. We extend this methodology for data filtering problems with unknown observation locations. We benchmark our algorithms on Linear Gaussian state space models against competing ensemble methods and demonstrate a significant improvement in both execution speed and accuracy. Finally, we implement a realistic case study on a high-dimensional rotating shallow water model (of about 104 - 105 dimensions) with real and synthetic data. The data is provided by the National Oceanic and Atmospheric Administration (NOAA) and contains observations from ocean drifters in a domain of the Atlantic Ocean restricted to the longitude and latitude intervals [-51◦,-41◦], [17◦,27◦] *** Codes 62M20, 60G35, 60J20, 94A12, 93E11, 65C40 © 2023, CC BY.

关键词： Location

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Local number fluctuations in ordered and disordered phases of water across temperatures: Higher-order moments and degrees of tetrahedrality

arXiv

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arXiv 2024年

作者： Klatt, Michael A. Kim, Jaeuk Gartner, Thomas E. Torquato, Salvatore Institute for AI Safety and Security Wilhelm-Runge-Str. 10 Ulm89081 Germany Institute for Material Physics in Space Köln51170 Germany Department of Physics Ludwig-Maximilians-Universität München Schellingstr. 4 Munich80799 Germany Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Materials Institute Princeton University PrincetonNJ08544 United States Department of Chemical & Biomolecular Engineering Lehigh University BethlehemPA18015 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The isothermal compressibility (i.e., the asymptotic number variance) of equilibrium liquid water as a function of temperature is minimal near ambient conditions. This anomalous non-monotonic temperature dependence is due to a balance between thermal fluctuations and the formation of tetrahedral hydrogen-bond networks. Since tetrahedrality is a many-body property, it will also influence the higher-order moments of density fluctuations, including the skewness and kurtosis. To gain a more complete picture, we examine these higher-order moments that encapsulate many-body correlations using a recently developed, advanced platform for local density fluctuations. We study an extensive set of simulated phases of water across a range of temperatures (80 K to 1600 K) with various degrees of tetrahedrality, including ice phases, equilibrium liquid water, supercritical water, and disordered nonequilibrium quenches. We find clear signatures of tetrahedrality in the higher-order moments, including the skewness and excess kurtosis, that scale for all cases with the degree of tetrahedrality. More importantly, this scaling behavior leads to non-monotonic temperature dependencies in the higher-order moments for both equilibrium and non-equilibrium phases. Specifically, at near-ambient conditions, the higher-order moments vanish most rapidly for large length scales, and the distribution quickly converges to a Gaussian in our metric. However, at non-ambient conditions, higher-order moments vanish more slowly and hence become more relevant especially for improving information-theoretic approximations of hydrophobic solubility. The temperature non-monotonicity that we observe in the full distribution across length-scales could shed light on water's nested anomalies, i.e., reveal new links between structural, dynamic, and thermodynamic anomalies. © 2024, CC BY-NC-ND.

关键词： Higher order statistics

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