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A review of the numerical methods for solving the binary Allen–Cahn equation

Physica A: Statistical Mechanics and its Applications 2025年 670卷

作者： Lee, Hyun Geun Li, Yibao Yang, Junxiang Kwak, Soobin Hwang, Youngjin Ham, Seokjun Kim, Hyundong Jyoti Nam, Yunjae Kim, Junseok Department of Mathematics Dongguk University Seoul04620 Korea Republic of School of Mathematics and Statistics Xi'an Jiaotong University Xi'an710049 China School of Computer Science and Engineering Faculty of Innovation Engineering Macau University of Science and Technology China Department of Mathematics Korea University Seoul02841 Korea Republic of Department of Mathematics and Physics Gangneung-Wonju National University Gangneung25457 Korea Republic of Smart infrastructure Gangneung-Wonju National University Gangneung25457 Korea Republic of The Institute of Basic Science Korea University Seoul02841 Korea Republic of Program in Actuarial Science and Financial Engineering Korea University Seoul02841 Korea Republic of

In this review, we present an overview of numerical methods to solve the binary Allen–Cahn (AC) equation, which is extensively used to model phase separation processes in materials science. It describes the time-dependent evolution of interfaces between two phases and accounts for both local reaction kinetics and diffusion effects. This equation plays a critical role in understanding the behavior of interfaces. The AC equation has various applications across fields such as materials science, physics, and biology, where it helps to analyze and predict phenomena such as phase transitions, grain boundary motion, and pattern formation in complex systems. Its importance lies in its ability to model the dynamics of interfaces and help the study of pattern formation and phase transitions in diverse environments. We discuss various computational methodologies developed for this important mathematical model and describe their strengths, limitations, and applications in diverse scientific domains. © 2025 Elsevier B.V.

关键词： Rate constants

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Feasibility of Inferring Spatial Transcriptomics from Single-Cell Histological Patterns for Studying Colon Cancer Tumor Heterogeneity

Feasibility of Inferring Spatial Transcriptomics from Single...

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18th International Joint Conference on Biomedical engineering Systems and Technologies, BIOSTEC 2025

作者： Fatemi, Michael Y. Lu, Yunrui Azher, Zarif L. Sharma, Cyril Feng, Eric Diallo, Alos B. Srinivasan, Gokul Rosner, Grace M. Pointer, Kelli B. Christensen, Brock C. Salas, Lucas A. Tsongalis, Gregory J. Palisoul, Scott M. Perreard, Laurent Kolling, Fred W. Vaickus, Louis J. Levy, Joshua J. University of Virginia CharlottesvilleVA United States Emerging Diagnostic and Investigative Technologies Department of Pathology and Laboratory Medicine Dartmouth Health LebanonNH United States Department of Computer Science Purdue University West LafayetteIN United States Thomas Jefferson High School for Science and Technology AlexandriaVA United States Department of Epidemiology Dartmouth College Geisel School of Medicine HanoverNH United States Program in Quantitative Biomedical Sciences Dartmouth College Geisel School of Medicine HanoverNH United States Department of Medicine Section of Radiology Oncology Dartmouth Health LebanonNH United States Department of Molecular and Cell Biology Dartmouth College Geisel School of Medicine HanoverNH United States Genomics Shared Resource Dartmouth Cancer Center LebanonNH United States Department of Dermatology Dartmouth Health LebanonNH United States Department of Pathology and Laboratory Medicine Cedars Sinai Medical Center Los AngelesCA United States Department of Computational Biomedicine Cedars Sinai Medical Center Los AngelesCA United States Division of Biology and Biological Engineering California Institute of Technology PasadenaCA United States

Spatial transcriptomics (ST) enables studying spatial organization of gene expression within tissues, offering insights into the molecular diversity of tumors. Recent methods have demonstrated the capability to disaggregate this information at subspot resolution by leveraging both expression and histological patterns. Elucidating such information from histology alone presents a significant challenge, but if solved can enable spatial molecular analysis at cellular resolution even where ST data is not available, reducing study costs. This study explores integrating single-cell histological and transcriptomic data to infer spatial mRNA expression patterns in colorectal cancer whole slide images. A cell-graph neural network algorithm was developed to align histological information extracted from detected cells with single cell RNA, facilitating the analysis of cellular groupings and gene relationships. We demonstrate that single-cell transcriptional heterogeneity within a spot could be predicted from histological markers extracted from cells detected within it. Our model exhibited proficiency in delineating overarching gene expression patterns across whole-slide images. This approach compared favorably to traditional computer vision methods which did not incorporate single cell expression during the model training. This innovative approach augments the resolution of spatial molecular assays utilizing histology as sole input through co-mapping of histological and transcriptomic datasets at the single-cell level. © 2025 by SCITEPRESS– Science and technology Publications, Lda.

关键词： Tumors

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Emergent dimer-model topological order and quasi-particle excitations in liquid crystals: combinatorial vortex lattices

arXiv

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arXiv 2025年

作者： Meng, Cuiling Wu, Jin-Sheng Kos, Žiga Dunkel, Jörn Nisoli, Cristiano Smalyukh, Ivan I. Department of Physics and Chemical Physics Program University of Colorado BoulderCO80309 United States Hiroshima University Hiroshima Higashihiroshima Japan Department of Mathematics Massachusetts Institute of Technology CambridgeMA02139 United States Faculty of Mathematics and Physics University of Ljubljana Ljubljana Slovenia Department of Condensed Matter Physics Jožef Stefan Institute Ljubljana Slovenia Theoretical Division Physics of Condensed Matter and Complex Systems Center For Nonlinear Studies Los Alamos National Laboratory Los AlamosNM87545 United States Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

Liquid crystals have proven to provide a versatile experimental and theoretical platform for studying topological objects such as vortices, skyrmions, and hopfions. In parallel, in hard condensed matter physics, the concept of topological phases and topological order has been introduced in the context of spin liquids to investigate emergent phenomena like quantum Hall effects and high-temperature superconductivity. Here, we bridge these two seemingly disparate perspectives on topology in physics. Combining experiments and simulations, we show how topological defects in liquid crystals can be used as versatile building blocks to create complex, highly degenerate topological phases, which we refer to as ‘Combinatorial Vortex Lattices’ (CVLs). CVLs exhibit extensive residual entropy and support locally stable quasi-particle excitations in the form of charge-conserving topological monopoles, which can act as mobile information carriers and be linked via Dirac strings. CLVs can be rewritten and reconfigured on demand, endowed with various symmetries, and modified through laser-induced topological surgery — an essential capability for information storage and retrieval. We demonstrate experimentally the realization, stability, and precise optical manipulation of CVLs, thus opening new avenues for understanding and technologically exploiting higher-hierarchy topology in liquid crystals and other ordered media. Copyright © 2025, The Authors. All rights reserved.

关键词： Laser surgery

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AI-driven 3D Spatial Transcriptomics

arXiv

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arXiv 2025年

作者： Almagro-Pérez, Cristina Song, Andrew H. Weishaupt, Luca Kim, Ahrong Jaume, Guillaume Williamson, Drew F.K. Hemker, Konstantin Lu, Ming Y. Singh, Kritika Chen, Bowen Le, Long Phi Baras, Alexander S. Jiang, Sizun Bashashati, Ali Liu, Jonathan T.C. Mahmood, Faisal Department of Pathology Mass General Brigham Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Pathology Pusan National University Busan Korea Republic of Department of Pathology and Laboratory Medicine Emory University School of Medicine AtlantaGA United States Department of Computer Science & Technology University of Cambridge Cambridge United Kingdom Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Rutgers Robert Wood Johnson Medical School New BrunswickNJ United States Department of Pathology Johns Hopkins Hospital BaltimoreMD United States Department of Biomedical Engineering Johns Hopkins Hospital BaltimoreMD United States Broad Institute of Harvard and MIT CambridgeMA United States Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Harvard Medical School BostonMA United States Department of Pathology Dana Farber Cancer Institute BostonMA United States Department of Pathology and Laboratory Medicine University of British Columbia VancouverBC Canada School of Biomedical Engineering University of British Columbia VancouverBC Canada Department of Mechanical Engineering Bioengineering Laboratory Medicine & Pathology University of Washington SeattleWA United States Harvard Data Science Initiative Harvard University CambridgeMA United States

A comprehensive three-dimensional (3D) map of tissue architecture and gene expression is crucial for illuminating the complexity and heterogeneity of tissues across diverse biomedical applications1. However, most spatial transcriptomics (ST) approaches remain limited to two-dimensional (2D) sections of tissue2–4. Although current 3D ST methods hold promise, they typically require extensive tissue sectioning, are complex, are not compatible with non-destructive 3D tissue imaging technologies, and often lack scalability5–8. Here, we present VOlumetrically Resolved Transcriptomics EXpression (VORTEX), an AI framework that leverages 3D tissue morphology and minimal 2D ST to predict volumetric 3D ST. By pretraining on diverse 3D morphology–transcriptomic pairs from heterogeneous tissue samples and then fine-tuning on minimal 2D ST data from a specific volume of interest, VORTEX learns both generic tissue-related and sample-specific morphological correlates of gene expression. This approach enables dense, high-throughput, and fast 3D ST, scaling seamlessly to large tissue volumes far beyond the reach of existing 3D ST techniques. By offering a cost-effective and minimally destructive route to obtaining volumetric molecular insights, we anticipate that VORTEX will accelerate biomarker discovery and our understanding of morphomolecular associations and cell states in complex tissues. Interactive 3D ST volumes can be viewed at https://***/. © 2025, CC BY-NC-ND.

关键词： Vortex flow

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Predicting the insulating paper state of the power transformer based on XGBoost/LightGBM models

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Scientific Reports 2025年第1期15卷 1-16页

作者： Sherif S. M. Ghoneim Mohammed Baz Ali Alzaed Yohannes Tesfaye Zewdie Department of Electrical Engineering College of Engineering Taif University Taif 21944 Saudi Arabia Department of Computer Engineering College of Computers and Information Technology Taif University Taif 21944 Saudi Arabia Architectural Engineering Program - Civil Engineering Department Faculty of Engineering Taif University Taif 21944 Saudi Arabia Department of Electrical and Computer Engineering Faculty of Technology Debre Markos University P. BOX 269 Debre Markos Ethiopia

Power transformer plays a crucial role in the power networks. Most of the transformer malfunctions was due to failure in the insulating systems. The utilities keen on the contentious operation of the power network, so early detection of the transformer faults avoiding the undesirable outage of the transformer from the service. The insulating paper state is an indication to the transformer health and aging of it may lead to failure of the transformer, so some periodic and routine test must be performed on the insulting oil to get information about the insulating paper condition. The value of the degree of polymerization (DP) is a key of the insulating paper state. Various recommended tests such as the dissolved gases (DGA), breakdown voltage (BDV), oil interfacial tension (IF), oil acidity (ACI), moisture content (MC), oil color (OC), dielectric loss (Tan δ), and furans concentration specifically (2-furfuraldehyde (2-FAL)) were carried out to correlate between these variables and the DP and then to the insulating oil state. The collected data from these tests were used to supply XGBoost/LightGBM to build artificial intelligence model to predict the insulating paper state. The results indicated that the great ability of the proposed model to predict the insulating state with high accuracy. Of these various configurations for these two classification models, one achieved perfect prediction accuracy (100%) of the insulating paper state prediction accuracy. The other configurations showed accuracy values from 1.0 down to 0.955.

关键词： Dissolved gas analysis Furnic compounds Insulating oil Insulating paper Power transformer XGBoost/LightGBM

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Obtaining bulk-like correlated oxide surfaces with protective caps

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Applied Physics Letters 2025年第16期126卷

作者： Cohen, Amit Baskin, Maria Shoham, Lishai Caspi, Shaked Shekhter, Pini Lee, Tien-Lin Chambers, Scott A. Kornblum, Lior Andrew and Erna Viterbi Department of Electrical and Computer Engineering Technion—Israel Institute of Technology Haifa32000-03 Israel The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology Technion—Israel Institute of Technology Haifa32000-03 Israel Wolfson Applied Materials Research Centre Tel Aviv University Tel Aviv Israel Diamond Light Source Ltd Harwell Science & Innovation Campus DidcotOX11 0DE United Kingdom Physical and Computational Sciences Directorate Pacific Northwest National Laboratory RichlandWA99352 United States

Functional oxides exhibit a diverse range of correlated electron phenomena, some of which are highly attractive for novel electronic, magnetic, and optical devices. Despite decades of advancement of our fundamental understanding of these materials, they consistently fall short of realizing their promise in functional devices. We identify a significant bottleneck toward device realization to be surface overoxidation. Protective caps can effectively prevent overoxidation, but their interfaces with functional oxides are not well understood. These interfaces are critical for effectively using functional oxides in field-effect devices, where "the interface is the device." This work addresses the chemistry and physics of the interface between protective caps and the correlated metal SrVO3, a model functional oxide. Our comparison of five different cap materials reveals effective protection and similar SrVO3 surface chemistry in all cases. Systematic comparisons of surface and bulk-sensitive photoelectron spectra reveal that negligible interface redox takes place, elucidating the cap-SrVO3 interface chemistry. This work demonstrates a robust and simple solution to the surface overoxidation problem in vanadates, paving the way toward effectively using these materials in field-effect devices. Our conclusions are general and can be applied to numerous other systems, thus moving oxide electronics closer to the realization of functional devices. © 2025 Author(s).

关键词： Redox reactions

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Measurement of peripheral nerve magnetostimulation thresholds of a head solenoid coil between 200 Hz and 88.1 kHz

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IEEE Journal of Translational engineering in Health and Medicine 2025年

作者： Barksdale, Alex C. Ferris, Natalie G. Mattingly, Eli Sliwiak, Monika Guerin, Bastien Wald, Lawrence L. Davids, Mathias Klein, Valerie MIT Department of Electrical Engineering and Computer Science Cambridge MA United States Martinos Center for Biomedical Imaging Charlestown MA United States Harvard University Harvard Graduate Program in Biophysics Cambridge MA United States Harvard-MIT Division of Health Sciences and Technology Boston MA United States Harvard Medical School Boston MA United States

Objective: Magnetic fields switching at kilohertz frequencies induce electric fields in the body, which can cause peripheral nerve stimulation (PNS). Although magnetostimulation has been extensively studied below 10 kHz, the behavior of PNS at higher frequencies remains poorly understood. This study aims to investigate PNS thresholds at frequencies up to 88.1 kHz and to explore deviations from the widely accepted hyperbolic strength-duration curve (SDC). Methods and procedures: PNS thresholds were measured in the head of 8 human volunteers using a solenoidal coil at 16 distinct frequencies, ranging from 200 Hz to 88.1 kHz. A hyperbolic SDC was used as a reference to compare the frequency-dependent behavior of PNS thresholds. Results: Contrary to the predictions of the hyperbolic SDC, PNS thresholds did not decrease monotonically with frequency. Instead, thresholds reached a minimum near 25 kHz, after which they increased by an average of 39% from 25 kHz to 88.1 kHz across subjects. This pattern indicates a significant deviation from previously observed behavior at lower frequencies. Conclusion: Our results suggest that PNS thresholds exhibit a non-monotonic frequency dependence at higher frequencies, diverging from the traditional hyperbolic SDC. These findings offer critical data for refining neurodynamic models and provide insights for setting PNS safety limits in applications like MRI gradient coils and magnetic particle imaging (MPI). Further investigation is needed to understand the biological mechanisms driving these deviations beyond 25 kHz. Clinical impact: These findings call for further basic research into biological mechanisms underlying high frequency PNS threshold trends, and supports refinement of safety guidelines for MRI and MPI systems for clinical implementation. © 2013 IEEE.

关键词： high frequency magnetostimulation magnetic particle imaging (MPI) magnetic resonance imaging (MRI) MRI gradient safety peripheral nerve stimulation

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An evolutionary game-theoretic approach for analysis of startups’ funding mechanisms considering their opportunistic and responsible behavior based on system dynamics

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Kybernetes 2025年

作者： Eghbali, Mohammad-Ali Rasti-Barzoki, Morteza Altmann, Jörn Department of Industrial Engineering Faculty of Computer and Industrial Engineering Birjand University of Technology Birjand Iran Department of Industrial and Systems Engineering Isfahan University of Technology Isfahan Iran Department of Industrial Engineering Technology Management Economics and Policy Program Seoul National University Seoul South Korea Technology Management Economics and Policy Program College of Engineering Seoul National University Seoul South Korea Integrated Major in Smart City Global Convergence Seoul National University Seoul South Korea

Purpose: Collaborating with startups is a fast track to green technological innovation (GTI) implementation for tech firms. On the other hand, startups’ opportunistic behavior during the collaboration could lead to GTI failure and a waste of tech firms’ investment. Accordingly, it is essential to conduct a dynamic analysis of the evolutionary behavior of tech firms and startups over time. In this regard, under government intervention, we consider a collaborative structure between two populations, including tech firms and startups. Design/methodology/approach: In this study, an evolutionary game structure based on system dynamics was developed to explain the tech firms’ and startups’ evolutionary trends, emphasizing investment mechanisms and the startup’s commitment level through a feedback process. For this purpose, the influence of the startups’green innovative efforts on the system’s evolution under two feedback loops was investigated. Furthermore, the effects of tech firms’ penalty strategies and government intervention on system evolutionary behavior was analyzed. Findings: The simulations revealed that applying the dynamic punishment policy can control the game’s oscillations in the evolutionary model and increase the startup’s and tech firm’s stability rate. When the penalty values change, and the startups’ credibility level is a variable under the impact of the green technological innovation features, it affects the evolutionary behavior of players over time through the positive feedback loop. It was also found that, despite the startups' opportunistic behaviors, effective government interference could raise the tech firms' tendency to invest in startups. Originality/value: Unlike previous studies, we focus on a dynamic analysis approach to investigate the collaborative structure between tech firms and startups. For the first time, we investigate the evolutionary behavior of startups and tech firms in positive and negative feedback structures to see how GTI f

关键词： Evolutionary game theory Green investment Green technological innovation Startup’s commitments Startup’s funding System dynamics

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ESG Investing: A Statistically Valid Approach to Data-Driven Decision Making and the Impact of ESG Factors on Stock Returns and Risk

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IEEE Access 2024年 12卷 69434-69444页

作者： Teja, Kamurthi Ravi Liu, Chuan-Ming National Taipei University of Technology International Program of Electrical Engineering and Computer Science Taipei10608 Taiwan National Taipei University of Technology Department of Computer Science and Information Engineering Taipei10608 Taiwan

This study examines the impact of environmental, social, and governance (ESG) factors on economic investment from a statistical perspective, aiming to develop a tested investment strategy that capitalizes on the connection between ESG factors and financial performance. ESG investing: A statistically valid approach to data-driven decision-making (ESGI-SVADDM) investment strategy is based on a rigorous, statistically valid approach that utilizes data, math, statistics, and data science libraries to drive investment decisions, eliminating the need for personal opinions and subjectivity. The process includes establishing an investment thesis, formulating testable hypotheses (HPS), retrieving and refining relevant data, calculating relevant measures, and testing and validating all hypotheses. The study uses S&P 500 stock data and ESG data from Sustainalytics to test the hypotheses. The empirical tests conducted revealed a negative correlation between ESG risk and expected returns, as well as a positive trend in the relationship between ESG risk and the overall risk of stocks. Moreover, the study found that higher ESG risk scores are associated with lower returns for investors, and that adopting a strategy of investing in stocks with low ESG risk and shorting stocks with high ESG risk yields superior returns compared to the market portfolio. © 2013 IEEE.

关键词： Investments

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Trade Ease with Machine Learning and AWS

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IEEE Access 2023年 11卷 25893-25905页

Global trading is undergoing significant changes, necessitating modifications to the trading strategies. This study presents a newly developed cloud-based trading strategy that uses Amazon Web Services (AWS), machine learning (ML), and data science to automate trading tasks. The study begins by creating a machine learning trading strategy using a customized deep neural network (DNN). The strategy was then tested using a trading station before deployment on a cloud machine. The execution of the strategy resulted in a total profit of 42.74526 USD, with a test accuracy score of 87.45% and a training accuracy score of 89.15% over 6047 epochs. The roadmap provides a step-by-step overview of the entire process from strategy development to execution. In addition, this study offers insights into related issues and solutions that can enhance the effectiveness of trading strategies. Overall, this study contributes significantly to the field of cloud-based trading strategies and opens avenues for future research. © 2013 IEEE.

关键词： Deep neural networks

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