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3D imaging lipidometry in single cell by in-flow holographic tomography

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Opto-Electronic Advances 2023年第1期6卷 10-25页

作者： Daniele Pirone Daniele Sirico Lisa Miccio Vittorio Bianco Martina Mugnano Danila del Giudice Gianandrea Pasquinelli Sabrina Valente Silvia Lemma Luisa Iommarini Ivana Kurelac Pasquale Memmolo Pietro Ferraro CNR-ISASI Institute of Applied Sciences and Intelligent Systems“E.Caianiello”Via Campi Flegrei 34PozzuoliNapoli 80078Italy Department of Electrical Engineering and Information Technologies University of Naples“FedericoⅡ”via Claudio 21Napoli 80125Italy Department of Chemical Materials and Production Engineering of the University of Naples FedericoⅡPiazzale Tecchio 80Napoli 80125Italy Department of Mathematics and Physics University of Campania“Luigi Vanvitelli”Caserta 81100Italy Biotechnology and Methods in Laboratory Medicine Department of ExperimentalDiagnostic and Specialty Medicine(DIMES)University of BolognaBologna 40126Italy Subcellular Nephro-Vascular Diagnostic Program Pathology Unit S.Orsola IRCCSUniversity of BolognaBologna 40126Italy Unit of Medical Genetics Department of Medical and Surgical Sciences(DIMEC)University of BolognaVia Massarenti 9Bologna 40138Italy Study and Research Center on Gynecological Neoplasias Department of Medical and Surgical Sciences(DIMEC)University of BolognaVia Massarenti 9Bologna 40138Italy Center for Applied Biomedical Research(CRBA) University of BolognaBologna 40138Italy Department of Pharmacy and Biotechnology(FABIT) University of BolognaBologna 40126Italy

The most recent discoveries in the biochemical field are highlighting the increasingly important role of lipid droplets(LDs)in several regulatory mechanisms in living *** are dynamic organelles and therefore their complete characterization in terms of number,size,spatial positioning and relative distribution in the cell volume can shed light on the roles played by *** now,fluorescence microscopy and transmission electron microscopy are assessed as the gold standard methods for identifying LDs due to their high sensitivity and ***,such methods generally only provide 2D assays and partial ***,both can be destructive and with low productivity,thus limiting analysis of large cell numbers in a *** we demonstrate for the first time the capability of 3D visualization and the full LD characterization in high-throughput with a tomographic phase-contrast flow-cytometer,by using ovarian cancer cells and monocyte cell lines as models.A strategy for retrieving significant parameters on spatial correlations and LD 3D positioning inside each cell volume is *** information gathered by this new method could allow more in depth understanding and lead to new discoveries on how LDs are correlated to cellular functions.

关键词： lipid droplets label-free phase-contrast imaging in-flow tomography 3D imaging

Dflow, a Python framework for constructing cloud-native AI-for-Science workflows

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arXiv 2024年

作者： Liu, Xinzijian Han, Yanbo Li, Zhuoyuan Fan, Jiahao Zhang, Chengqian Zeng, Jinzhe Shan, Yifan Yuan, Yannan Xu, Wei-Hong Liu, Yun-Pei Zhang, Yuzhi Wen, Tongqi York, Darrin M. Zhong, Zhicheng Zheng, Hang Cheng, Jun Zhang, Linfeng Wang, Han DP Technology Beijing100080 China Institute of Molecular Science and Applied Chemistry School of Chemistry Xi'an Jiaotong University Xi'An710049 China Department of Mechanical Engineering The University of Hong Kong Hong Kong School of Physics Peking University Beijing100871 China AI for Science Institute Beijing100080 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Laboratory for Biomolecular Simulation Research Center for Integrative Proteomics Research Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854-8087 United States Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China IKKEM Xiamen361005 China State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials College of Chemistry and Chemical Engineering Xiamen University Xiamen361005 China Department of Physics University of Science and Technology of China Hefei230026 China Suzhou Institute for Advanced Research University of Science and Technology of China Suzhou215123 China Institute of Artificial Intelligence Xiamen University Xiamen361005 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100094 China

In the AI-for-science era, scientific computing scenarios such as concurrent learning and high-throughput computing demand a new generation of infrastructure that supports scalable computing resources and automated workflow management on both cloud and high-performance supercomputers. Here we introduce Dflow, an open-source Python toolkit designed for scientists to construct workflows with simple programming interfaces. It enables complex process control and task scheduling across a distributed, heterogeneous infrastructure, leveraging containers and Kubernetes for flexibility. Dflow is highly observable and can scale to thousands of concurrent nodes per workflow, enhancing the efficiency of complex scientific computing tasks. The basic unit in Dflow, known as an Operation (OP), is reusable and independent of the underlying infrastructure or context. Dozens of workflow projects have been developed based on Dflow, spanning a wide range of projects. We anticipate that the reusability of Dflow and its components will encourage more scientists to publish their workflows and OP components. These components, in turn, can be adapted and reused in various contexts, fostering greater collaboration and innovation in the scientific community. Copyright © 2024, The Authors. All rights reserved.

关键词： Reusability

Interlayer antisynchronization in degree-biased duplex networks

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arXiv 2023年

作者： Chowdhury, Sayantan Nag Rakshit, Sarbendu Hens, Chittaranjan Ghosh, Dibakar Department of Environmental Science and Policy University of California DavisCA95616 United States @ Indian Statistical Institute 203 B. T. Road Kolkata700108 India Department of Mechanical Engineering University of California RiversideCA92521 United States Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Gachibowli Hyderabad500032 India Physics and Applied Mathematics Unit Indian Statistical Institute 203 B. T. Road Kolkata700108 India

With synchronization being one of nature’s most ubiquitous collective behaviors, the field of network synchronization has experienced tremendous growth, leading to significant theoretical developments. However, most of these previous studies consider uniform connection weights and undirected networks with positive coupling. In the present article, we incorporate the asymmetry in a two-layer multiplex network by assigning the ratio of the adjacent nodes’ degrees as the weights to the intralayer edges. Despite the presence of degree-biased weighting mechanism and attractive-repulsive coupling strengths, we are able to find the necessary conditions for intralayer synchronization and interlayer antisynchronization and test whether these two macroscopic states can withstand demultiplexing in a network. During the occurrence of these two states, we analytically calculate the oscillator’s amplitude. In addition to deriving the local stability conditions for interlayer antisynchronization via the master stability function approach, we also construct a suitable Lyapunov function to determine a sufficient condition for global stability. We provide numerical evidence to show the necessity of negative interlayer coupling strength for the occurrence of antisynchronization, and such repulsive interlayer coupling coefficients can not destroy intralayer synchronization. © 2023, CC BY.

关键词： Synchronization

General Matrix Representation For Generalized B-Splines and its Application

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SSRN

SSRN 2023年

作者： Guo, Huayuan Liu, Minchao Qin, Guiming Qin, Kaihuai He, Kunlun Medical Big Data Research Center Medical Innovation Research Division Chinese PLA General Hospital. Beijing100853 China Medical Artificial Intelligence Research Center Medical Innovation Research Division Chinese PLA General Hospital Beijing100853 China Department of Information Medical Supplies Center of Chinese PLA General Hospital Beijing100853 China Institute of Applied Physics and computational Mathematics Beijing100091 China Department of Computer science and technology Tsinghua University Beijing100084 China

Classical B-splines based on deBoor-Cox algorithm is widely used, but its recursive calculation is time-consuming and its shape control capability still needs to be improved. To address the problem, by incorporated both core functions and Toeplitz matrix theory into the deBoor-Cox recursive formula, a novel set of basis matrix formula to calculate generalized B-splines of arbitrary order is proposed to realize the general matrix representation of three types of curves, including non-uniform generalized B-splines,uniform generalized B-splines and generalized piecewise Bézier. Furthermore, based on this general matrix, we developed the shape-controllable algorithms for curve generation and curve/surface interpolation. Experiments show that our basis matrix method outperforms classical method in terms of computational time and shape controllability for curve and surface modeling. Therefore, this novel method can further enrich the B-splines modeling theory and has good application potential. © 2023, The Authors. All rights reserved.

关键词： Matrix algebra

A fourth-order phase-field fracture model: Formulation and numerical solution using a continuous/discontinuous Galerkin method

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Journal of the Mechanics and physics of Solids 2022年 165卷 1页

作者： Svolos, Lampros Mourad, Hashem M. Manzini, Gianmarco Garikipati, Krishna Fluid Dynamics and Solid Mechanics T-3 Theoretical Division Los Alamos National Laboratory Los Alamos NM United States Applied Mathematics and Plasma Physics T-5 Theoretical Division Los Alamos National Laboratory Los Alamos NM United States Department of Mechanical Engineering University of Michigan Ann Arbor MI United States Department of Mathematics University of Michigan Ann Arbor MI United States Michigan Institute for Computational Discovery & Engineering University of Michigan Ann Arbor MI United States

Modeling crack initiation and propagation in brittle materials is of great importance to be able to predict sudden loss of load-carrying capacity and prevent catastrophic failure under severe dynamic loading conditions. Second-order phase-field fracture models have gained wide adoption given their ability to capture the formation of complex fracture patterns, e.g. via crack merging and branching, and their suitability for implementation within the context of the conventional finite element method. Higher-order phase-field models have also been proposed to increase the regularity of the exact solution and thus increase the spatial convergence rate of its numerical approximation. However, they require special numerical techniques to enforce the necessary continuity of the phase field solution. In this paper, we derive a fourth-order phase-field model of fracture in two independent ways;namely, from Hamilton's principle and from a higher-order micromechanics-based approach. The latter approach is novel, and provides a physical interpretation of the higher-order terms in the model. In addition, we propose a continuous/discontinuous Galerkin (C/DG) method for use in computing the approximate phase-field solution. This method employs Lagrange polynomial shape functions to guarantee C0-continuity of the solution at inter-element boundaries, and enforces the required C1 regularity with the aid of additional variational and interior penalty terms in the weak form. The phase-field equation is coupled with the momentum balance equation to model dynamic fracture problems in hyper-elastic materials. Two benchmark problems are presented to compare the numerical behavior of the C/DG method with mixed finite element methods. © 2022 Elsevier Ltd

关键词： Fracture

Quantum interferences between rescattering orbits with multiexcitation channels in the recollision excitation process of nonsequential double ionization

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Physical Review A 2021年第3期103卷 033111-033111页

作者： Yuna Yang Mingqing Liu Xiaolei Hao Jing Chen Institute of Applied Physics and Computational Mathematics Beijing 100088 China College of Science Tianjin University of Technology Tianjin 300384 China Institute of Theoretical Physics and Department of Physics State Key Laboratory of Quantum Optics and Quantum Optics DevicesCollaborative Innovation Center of Extreme Optics Shanxi University Taiyuan 030006 China Center for Advanced Material Diagnostic Technology Shenzhen Technology University Shenzhen 518118 China

Based on the strong-field approximation (SFA), we investigate the interference between different returning orbits of the rescattering electron in nonsequential double ionization. We find that the effect of interference is negligible in the recollision-impact ionization process but is prominent in the recollision excitation with subsequent ionization process and induces fast oscillation with constant period in the laser intensity dependence of the asymmetry parameter. The dominant contribution to the fast oscillation comes from the mixed interference between different pairs of returning orbits in different excitation channels. However, the oscillation disappears after laser focus averaging is performed due to its rather small period.

关键词： Atomic & molecular processes in external fields Multiphoton or tunneling ionization & excitation

Obstacles on the Pathway Towards Chemical programmability Using Agglomerations of Droplets 15th

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Obstacles on the Pathway Towards Chemical Programmability Us...

15th International Workshop on Artificial Life and Evolutionary Computation, WIVACE 2021

作者： Schneider, Johannes Josef Faggian, Alessia Matuttis, Hans-Georg Barrow, David Anthony Li, Jin Holler, Silvia Casiraghi, Federica Sanahuja, Lorena Cebolla Hanczyc, Martin Michael Eschle, Patrik Weyland, Mathias Sebastian Flumini, Dandolo Eggenberger Hotz, Peter Füchslin, Rudolf Marcel Institute of Applied Mathematics and Physics School of Engineering Zurich University of Applied Sciences Technikumstr. 9 Winterthur8401 Switzerland Laboratory for Artificial Biology Department of Cellular Computational and Integrative Biology University of Trento Via Sommarive 9 Povo38123 Italy Department of Mechanical Engineering and Intelligent Systems The University of Electrocommunications Chofu Chofugaoka 1-5-1 Tokyo182-8585 Japan Laboratory for Microfluidics and Soft Matter Microengineering Cardiff School of Engineering Cardiff University Queen’s Buildings 14-17 The Parade CardiffCF24 3AA United Kingdom Chemical and Biological Engineering University of New Mexico MSC01 1120 AlbuquerqueNM87131-0001 United States European Centre for Living Technology Ca’ Bottacin Dorsoduro 3911 Calle Crosera Venice30123 Italy

ISBN: (纸本)9783031239281

We aim at planning and creating specific agglomerations of droplets to study synergic communication using these as programmable units. In this paper, we give an overview of preliminary obstacles for the various research issues, namely of how to create droplets, how to set up droplet agglomerations using DNA technology, how to prepare them for confocal microscopy, how to make a computer see droplets on photos, how to analyze networks of droplets, how to perform simulations mimicking experiments, and how to plan specific agglomerations of droplets. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Drops

Super-Resolution without High-Resolution Labels for Black Hole Simulations

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arXiv 2024年

作者： Helfer, Thomas Edwards, Thomas D.P. Dafflon, Jessica Wong, Kaze W.K. Olson, Matthew Lyle Institute for Advanced Computational Science Stony Brook University Stony BrookNY11794 United States William H. Miller III Department of Physics and Astronomy Johns Hopkins University BaltimoreMD21218 United States Valence Labs 6666 Rue Saint-Urbain MontrealQCH2S 3H1 Canada Department of Applied Mathematics and Statistics Johns Hopkins University BaltimoreMD21218 United States Data Science and AI Institute Johns Hopkins University BaltimoreMD21218 United States Center for Computational Astrophysics Flatiron Institute New YorkNY10010 United States Intel Labs Santa ClaraCA United States

Generating high-resolution simulations is key for advancing our understanding of one of the universe's most violent events: Black Hole mergers. However, generating Black Hole simulations is limited by prohibitive computational costs and scalability issues, reducing the simulation's fidelity and resolution achievable within reasonable time frames and resources. In this work, we introduce a novel method that circumvents these limitations by applying a super-resolution technique without directly needing high-resolution labels, leveraging the Hamiltonian and momentum constraints-fundamental equations in general relativity that govern the dynamics of spacetime. We demonstrate that our method achieves a reduction in constraint violation by one to two orders of magnitude and generalizes effectively to out-of-distribution simulations. Copyright © 2024, The Authors. All rights reserved.

关键词： Black holes

Autonomous Electron Tomography Reconstruction with Machine Learning

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arXiv 2023年

作者： Millsaps, William Schwartz, Jonathan Di, Zichao Wendy Jiang, Yi Hovden, Robert Department of Nuclear Engineering & Radiological Sciences University of Michigan Ann ArborMI United States Department of Materials Science and Engineering University of Michigan Ann ArborMI United States Mathematics and Computer Science Division Argonne National Laboratory LemontIL United States Advanced Photon Source Facility Argonne National Laboratory LemontIL United States Applied Physics Program University of Michigan Ann ArborMI United States

This manuscript is published in Microscopy and Microanalysis (DOI: 10.1093/micmic/ozad083). Modern electron tomography has progressed to higher resolution at lower doses by leveraging compressed sensing methods that minimize total variation (TV). However, these sparsity-emphasized reconstruction algorithms introduce tunable parameters that greatly influence the reconstruction quality. Here, Pareto front analysis shows that high-quality tomograms are reproducibly achieved when TV minimization is heavily weighted. However, in excess, compressed sensing tomography creates overly smoothed 3D reconstructions. Adding momentum to the gradient descent during reconstruction reduces the risk of over-smoothing and better ensures that compressed sensing is well behaved. For simulated data, the tedious process of tomography parameter selection is efficiently solved using Bayesian optimization with Gaussian processes. In combination, Bayesian optimization with momentum-based compressed sensing greatly reduces the required compute time-an 80% reduction was observed for the 3D reconstruction of SrTiO3 nanocubes. Automated parameter selection is necessary for large scale tomographic simulations that enable the 3D characterization of a wider range of inorganic and biological materials. © 2023, CC BY.

关键词： Compressed sensing