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Implicit Asymptotic Preserving Method for Linear Transport Equations

Communications in computational Physics 2017年第6期22卷 157-181页

作者： Qin Li Li Wang Mathematics Department University of Wisconsin-Madison480 Lincoln Dr.MadisonWI 53705USA Departments of Mathematics and Computational Data-Enabled Science and Engineering Program State University of New York at Buffalo244 Mathematics BuildingBuffaloNY 14260USA The Optimization Group TheWisconsin Institute ofDiscoveryMadisonWI 53715USA

The computation of the radiative transfer equation is expensive mainly due to two stiff terms:the transport term and the collision *** stiffness in the former comes from the fact that particles(such as photons)travel at the speed of light,while that in the latter is due to the strong scattering in the optically thick *** study the fully implicit scheme for this equation to account for the *** main challenge in the implicit treatment is the coupling between the spacial and angular coordinates that requires the large size of the to-be-inverted matrix,which is also ill-conditioned and not necessarily *** main idea is to utilize the spectral structure of the ill-conditioned matrix to construct a pre-conditioner,which,along with an exquisite split of the spatial and angular dependence,significantly improve the condition number and allows a matrix-free *** also design a fast solver to compute this pre-conditioner explicitly in *** method is shown to be efficient in both diffusive and free streaming limit,and the computational cost is comparable to the state-of-the-art *** examples including anisotropic scattering and two-dimensional problems are provided to validate the effectiveness of our method.

关键词： Implicitmethod asymptotic preserving pre-conditioner diffusive regime free streaming limit

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A numerical study of bayesian inference of surface catalycity in low speed reacting flow using laser absorption spectroscopy 12th

A numerical study of bayesian inference of surface catalycit...

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12th AIAA/ASME Joint Thermophysics and Heat Transfer Conference, 2018

作者： Adowski, Timothy R. Bauman, Paul T. Department of Mechanical and Aerospace Engineering University at Buffalo BuffaloNY14260-4400 United States Department of Mechanical and Aerospace Engineering Computational and Data-Enabled Science and Engineering University at Buffalo BuffaloNY14260-4400 United States

ISBN: (数字)9781624105524

ISBN: (纸本)9781624105524

In this work, we investigate the statistical inference of surface chemistry parameters from noisy data stemming from tunable diode laser absorption spectroscopy (TDLAS). We leverage previous work whereby TDLAS is simulated in two-dimensional finite element simulations of low speed reacting flow. In particular, we compute the attenuation of laser intensity along an optical path that passes through carbon monoxide CO gas generated by a reacting specimen. The goal is to be able to infer parameters related to the surface chemistry based on the laser attenuation data. Using baseline values from the literature, we numerically simulate TDLAS data and add statistical noise. We then use this synthetic data to infer parameters in various surface chemistry models to demonstrate the feasibility of the methodology. © 2018 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

关键词： Surface chemistry

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Artificial intelligence for modelling infectious disease epidemics

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Nature 2025年第8051期638卷 623-635页

作者： Kraemer, Moritz U. G. Tsui, Joseph L.-H. Chang, Serina Y. Lytras, Spyros Khurana, Mark P. Vanderslott, Samantha Bajaj, Sumali Scheidwasser, Neil Curran-Sebastian, Jacob Liam Semenova, Elizaveta Zhang, Mengyan Unwin, H. Juliette T. Watson, Oliver J. Mills, Cathal Dasgupta, Abhishek Ferretti, Luca Scarpino, Samuel V. Koua, Etien Morgan, Oliver Tegally, Houriiyah Paquet, Ulrich Moutsianas, Loukas Fraser, Christophe Ferguson, Neil M. Topol, Eric J. Duchêne, David A. Stadler, Tanja Kingori, Patricia Parker, Michael J. Dominici, Francesca Shadbolt, Nigel Suchard, Marc A. Ratmann, Oliver Flaxman, Seth Holmes, Edward C. Gomez-Rodriguez, Manuel Schölkopf, Bernhard Donnelly, Christl A. Pybus, Oliver G. Cauchemez, Simon Bhatt, Samir Pandemic Sciences Institute University of Oxford Oxford United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Electrical Engineering and Computer Science University of California Berkeley Berkeley CA United States UCSF UC Berkeley Joint Program in Computational Precision Health Berkeley CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Section of Epidemiology Department of Public Health University of Copenhagen Copenhagen Denmark Oxford Vaccine Group University of Oxford and NIHR Oxford Biomedical Research Centre Oxford United Kingdom Department of Epidemiology and Biostatistics Imperial College London London United Kingdom Department of Computer Science University of Oxford Oxford United Kingdom School of Mathematics University of Bristol Bristol United Kingdom MRC Centre for Global Infectious Disease Analysis School of Public Health Imperial College London London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Doctoral Training Centre University of Oxford Oxford United Kingdom Institute for Experiential AI Northeastern University MA Boston Thailand Santa Fe Institute Santa Fe NM United States World Health Organization Regional Office for Africa Brazzaville Congo WHO Hub for Pandemic and Epidemic Intelligence Health Emergencies Programme World Health Organization Berlin Germany Centre for Epidemic Response and Innovation (CERI) School for Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa African Institute for Mathematical Sciences (AIMS) South Africa Muizenberg Cape Town South Africa Genomics England London United Kingdom Scripps Research La Jolla CA United States Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland The Ethox Centre Nuffield

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI. © Springer Nature Limited 2025.

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High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH

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Cell 2025年

作者： Zhu, Yanyu Balaji, Ashwin Han, Mengting Andronov, Leonid Roy, Anish R. Wei, Zheng Chen, Crystal Miles, Leanne Cai, Sa Gu, Zhengxi Tse, Ariana Yu, Betty Chentzu Uenaka, Takeshi Lin, Xueqiu Spakowitz, Andrew J. Moerner, W.E. Qi, Lei S. Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Chemistry Stanford University Stanford 94305 CA United States Biophysics PhD Program Stanford University Stanford 94305 CA United States Computational Biology Program Public Health Sciences Division and Translational Data Science IRC Fred Hutchinson Cancer Center Seattle 98109 WA United States Department of Chemical Engineering Stanford University Stanford 94305 CA United States Department of Materials Science and Engineering Stanford University Stanford 94305 CA United States Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology Stanford University School of Medicine Stanford 94305 CA United States Sarafan ChEM-H Stanford University Stanford 94305 CA United States Chan Zuckerberg Biohub San Francisco 94080 CA United States

Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease. © 2025 Elsevier Inc.

关键词： CRISPR imaging DNA communication dynamic tracking enhancer-promoter interaction high-resolution imaging live DNA imaging non-repetitive genome imaging Oligo-LiveFISH polymer modeling primary cell

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Multimodal identification of the mouse brain using simultaneous Ca²⁺ imaging and fMRI

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Communications Biology 2025年第1期8卷 1-14页

作者： Mandino, Francesca Horien, Corey Shen, Xilin Desrosiers-Grégoire, Gabriel Luo, Wendy Markicevic, Marija Constable, R. Todd Papademetris, Xenophon Chakravarty, Mallar M. Betzel, Richard F. Lake, Evelyn M. R. Department of Radiology and Biomedical Imaging Yale University School of Medicine New Haven CT United States Interdepartmental Neuroscience Program Yale University School of Medicine New Haven CT United States MD/PhD program Yale University School of Medicine New Haven CT United States Computational Brain Anatomy Laboratory Douglas Mental Health University Institute Montreal QC Canada Integrated Program in Neuroscience McGill University Montreal QC Canada Department of Biomedical Engineering Yale University School of Medicine New Haven CT United States Department of Neurosurgery Yale University School of Medicine New Haven CT United States Deparment of Biomedical Informatics and Data Science Yale University New Haven CT United States Department of Psychological and Brain Sciences Indiana University Bloomington IN United States Wu Tsai Institute Yale University New Haven CT United States

Individual differences in neuroimaging are of interest to clinical and cognitive neuroscientists based on their potential for guiding the personalized treatment of various heterogeneous neurological conditions and diseases. Despite many advantages, the prevailing modality in this field—blood-oxygen-level-dependent (BOLD) functional magnetic resonance imaging (fMRI)—suffers from low spatiotemporal resolution and specificity as well as a propensity for noise and spurious signal corruption. To better understand individual differences in BOLD-fMRI data, we can use animal models where fMRI, alongside complementary but more invasive contrasts, can be accessed. Here, we apply simultaneous wide-field fluorescence calcium imaging and BOLD-fMRI in mice to interrogate individual differences using a connectome-based identification framework adopted from the human fMRI literature. This approach yields high spatiotemporal resolution cell-type specific signals (here, from glia, excitatory, as well as inhibitory interneurons) from the whole cortex. We found mouse multimodal connectome-based identification to be successful and explored various features of these data. © The Author(s) 2025.

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Modeling laser attenuation in reacting flows using adaptive finite elements 55

Modeling laser attenuation in reacting flows using adaptive ...

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55th AIAA Aerospace sciences Meeting

作者： Bauman, Paul T. Adowski, Timothy R. Department of Mechanical and Aerospace Engineering Computational and Data-Enabled Science and Engineering University at Buffalo State University of New York BuffaloNY14260-4400 United States Department of Mechanical and Aerospace Engineering University at Buffalo State University of New York BuffaloNY14260-4400 United States

ISBN: (数字)9781624104473

ISBN: (纸本)9781624104473

In this work, we demonstrate the use of adaptive finite element analysis in low speed chemically reacting flows to compute the attenuation of laser intensity through an arbitrary path in the domain. We use adjoint-based error estimates to estimate the error in the computed intensity and drive adaptive mesh refinement. We discuss details of the implementation with the GRINS multiphysics framework, built on the libMesh finite element library. We present an example illustrating the adjoint solution and resulting adapted mesh for a laser attenuation quantity-of-interest in a two-dimensional reacting flow with heterogeneous carbon surface chemistry. © 2017 by Paul T. Bauman.

关键词： Chemically Reacting Flow Diode Lasers Adaptive Mesh Refinement Finite Element Formulation Doppler Broadening Beer Lambert Law Computing Thermal Boundary Condition Navier Stokes Equations Mathematical Models

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Automated, high throughput exploration of process–structure–property relationships using the MapReduce paradigm

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Materials Discovery 2015年 1卷 21-28页

作者： Wodo, Olga Zola, Jaroslaw Sarath Pokuri, Balaji Sesha Du, Pengfei Ganapathysubramanian, Baskar University at Buffalo Materials Design and Innovation Department Buffalo United States University at Buffalo Mechanical and Aerospace Engineering Department Buffalo United States University at Buffalo Computational and Data-Enabled Science and Engineering Program Buffalo United States University at Buffalo Computer Science and Engineering Department Buffalo United States University at Buffalo Biomedical Informatics Department Buffalo United States Iowa State University Mechanical Engineering Department Ames United States Iowa State University Electrical and Computer Engineering Department Ames United States

The microstructure of a material intimately affects the performance of a device made from this material. The microstructure, in turn, is affected by the processing pathway used to fabricate the device. This forms the process–structure–property triangle that is central to material science. There has been increasing interest to comprehensively understand and subsequently exploit process–structure–property (PSP) relationships to design processing pathways that result in tailored microstructures exhibiting optimal properties. However, unraveling process–structure–property relationships usually requires systematic and tedious combinatorial search of process and system variables to identify the microstructures that are produced. This is further complicated by the necessity to interrogate the properties of the huge set of corresponding microstructures. Motivated by this challenge, we focus on developing a generic methodology to establish and explore PSP pathways. We leverage recent advances in high performance computing (HPC) and high throughput computing (HTC) with the premise that a domain expert should be able to focus on domain specific PSP problems while the highly specialized HPC/HTC knowledge needed to approach such problems should be hidden from the domain expert. Our hypothesis is that PSP exploration can be naturally formulated in terms of a standard paradigm in cloud computing, namely the MapReduce programming model. We show how reformulating PSP exploration into a MapReduce workflow enables us to take advantage of advances in cloud computing while requiring minimal specialized knowledge of HPC. We illustrate this generic approach by exploring PSP relationships relevant to organic photovoltaics. We focus on identifying microstructural traits that correlate with specific properties of the photovoltaic process: exciton generation, exciton dissociation and charge generation. We integrate a graph-based microstructure characterization tool, and a microstructure-aware

关键词： Drift diffusion model High throughput analysis MapReduce paradigm Organic solar cells Process–structure–processing Thermal annealing

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A Comparison of Global Sensitivity Methods for Power Systems

A Comparison of Global Sensitivity Methods for Power Systems

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International Conference on System Reliability and science (ICSRS)

作者： Ruilong Yue Hui Duan Giray Ökten Bahri Uzunoğlu Department of Mathematics Florida State University USA Department of Electrical Engineering Computational and Data-Enabled Science and Engineering in Energy Systems Uppsala University Sweden

The sensitivity of power system operations uncertainties that originate from distributed renewable generation, natural disasters like hurricanes, and changing loads such as vehicle charging needs careful engineering for reliable, resilient and robust power systems. The power system is a global sensitivity problem since each input uncertainty varies the output and all the variables simultaneously that have higher order interactions between inputs, unlike local sensitivity. The article assesses and compares the global sensitivity methods of Sobol’ sensitivity indices, the activity scores of the active subspace method, and Shapley values, to assess the importance of input parameters in the IEEE 14-bus modified test system. The limitations and advantages of each approach are illustrated to reduce the complexity of the model by performing uncertainty quantification for the output by global sensitivity indices in the IEEE 14-bus modified test system.

关键词： Renewable energy sources Sensitivity Uncertainty Wind power generation Reliability engineering Hurricanes Safety

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Ensemble Filter Scenario Based Control on Linearized Power System Manifold

Ensemble Filter Scenario Based Control on Linearized Power S...

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International Conference on System Reliability and science (ICSRS)

作者： Bahri Uzunoğlu Department of Electrical Engineering Computational and data-enabled science and engineering in energy systems Uppsala University Sweden Department of Mathematics Florida State University USA

ISBN: (数字)9798350354508

ISBN: (纸本)9798350354515

This article integrates the widely recognised ensemble filters that are employed for power system state estimation and their ensemble scenarios to controls for power systems linearised on manifolds. The approach has the effect of directly providing constraint scenarios for any optimal real-time fast power system management for any ensemble-based state estimator used in the power system, thereby reducing the computational task for both radial and meshed power systems and addressing the computational needs of stochastic external state parameter that is not controlled by the grid operator. New and unparalleled obstacles have surfaced in the recent past for power systems. Tighter guidelines for grid reliability and service quality, the growing spread of electric mobility that has given rise to a new class of intermittent loads with distinct spatiotemporal patterns, and the growing use of distributed microgenerators from renewable power sources-which are frequently characterised by unpredictable behavior-are some of these challenges. For proof of concept, the method is shown on a simple example.

关键词： Manifolds Renewable energy sources Uncertainty Decision making Transforms Power systems Spatiotemporal phenomena Kalman filters Reliability State estimation

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