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cytoNet: Spatiotemporal network analysis of cell communities (vol 18, e1009846, 2022)

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PLOS COMPUTATIONAL BIOLOGY 2022年第11期18卷 e1009846页

作者： Mahadevan, A. S. Long, B. L. Hu, C. W. Ryan, D. T. Grandel, N. E. Department of Bioengineering University of Pennsylvania Philadelphia Pennsylvania United States of America. Department of Bioengineering Rice University Houston Texas United States of America. Systems Synthetic and Physical Biology Program Rice University Houston Texas United States of America. Department of Biomedical Engineering University of Texas at San Antonio San Antonio Texas United States of America. Biophysics Graduate Program University of California Berkeley California United States of America. Department of Oral & Maxillofacial Surgery University of Texas Health Science Center at San Antonio San Antonio Texas United States of America. Department of Electrical and Computer Engineering Rice University Houston Texas United States of America.

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNet's capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin α4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains.

关键词： Calcium imaging Fluorescence imaging Growth factors Centrality Cell cycle and cell division Endothelial cells Network analysis Stem cells

A fiber-optic-distributed temperature mapping technique to characterize shell solidification in peritectic-grade steels

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A fiber-optic-distributed temperature mapping technique to c...

AISTech 2021 Iron and Steel Technology Conference

作者： Balogun, Damilola Roman, Muhammad Bartlett, Laura O'Malley, Ronald Gerald, Rex E. Huang, Jie Department of Materials Science and Engineering Missouri University of Science and Technology RollaMO65409 United States Department of Electrical and Computer Engineering Missouri University of Science and Technology RollaMO65409 United States Missouri University of Science and Technology RollaMO65409 United States

ISBN: (纸本)9781935117933

The quality of continuously cast steels is governed by events that occur during the initial stage of solidification in the mold, where the first layer of steel shell forms. In peritectic steels, solidification is influenced by the nature of the ferrite to austenite transformation, which is an antecedent for shell buckling and non-uniform growth during continuous casting of these steel grades. A dip test, which employs a copper mold instrumented with distributed fiber-optic sensors, has been developed to map closely spaced thermal features that are induced by the peritectic transformation. The magnitude of unevenness in shell thickness was also obtained. © 2021 by the Association for Iron & Steel Technology.

关键词： Solidification

Indirect Tunneling Enabled Spontaneous Time-Reversal Symmetry Breaking and Josephson Diode Effect in TiN/Al2O3/Hf0.8Zr0.2O2/Nb tunnel junctions

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arXiv 2025年

作者： Ding, Shaoqing Yao, Jinyuan Bi, Zhen Tran, Quyen Liu, Bangzhi Li, Qi Trolier-McKinstry, Susan Jackson, Thomas N. Liu, Ying Department of Physics The Pennsylvania State University University ParkPA16802 United States Materials Research Institute The Pennsylvania State University University ParkPA16802 United States School of Electrical Engineering and Computer Science The Pennsylvania State University University ParkPA16802 United States Materials Science and Engineering Department The Pennsylvania State University University ParkPA16802 United States

Josephson diode (JD) effect found in Josephson tunnel junctions (JTJs) has attracted a great deal of attention due to its importance for developing superconducting circuitry based quantum technologies. So far, the highly desirable electrical control of the JD effect has not been demonstrated in any JTJ prepared using techniques employed in the semiconductor industry. We report the fabrication of JTJs featuring a composite tunnel barrier of Al2O3 and Hf0.8Zr0.2O2 prepared by complementary-metal-oxide-semiconductor (CMOS) compatible atomic layer deposition (ALD). These JTJs were found to show the JD effect in nominally zero magnetic fields with nonreciprocity controllable via an electric training current, yielding a surprisingly large diode efficiency, previously unattained. The quasiparticle tunneling, through which the Josephson coupling in a JTJ is established, was found to show no nonreciprocity. We attribute these observations to the simultaneous presence of positive and negative Josephson couplings, with the latter originating from indirect tunneling. The resulted spontaneous time-reversal symmetry breaking and the double-minima washboard potential for the ensemble averaged phase difference in the resistively and capacitively shunted junction (RCSJ) model are shown to fully account for the experimentally observed JD effect. Copyright © 2025, The Authors. All rights reserved.

关键词： Tunnel junctions

Quantitative Modeling of Point Defects in β-Ga2O3 Combining Hybrid Functional Energetics with Semiconductor and Processes Thermodynamics

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arXiv 2025年

作者： Arnab, Khandakar Aaditta Stephens, Megan Maxfield, Isaac Lee, Channyung Ertekin, Elif Frodason, Ymir K. Varley, Joel B. Scarpulla, Michael A. Department of Materials Science and Engineering University of Utah Salt Lake CityUT84112 United States Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Materials Research Laboratory University of Illinois at Urbana-Champaign UrbanaIL61801 United States Centre for Materials Science and Nanotechnology Physics University of Oslo Oslo Norway Lawrence Livermore National Laboratory LivermoreCA93106 United States Department of Electrical and Computer Engineering University of Utah Salt Lake CityUT84112 United States

β-gallium oxide (β-Ga2O3) is of high interest for power electronics because of its unique combination of melt growth, epitaxial growth, n-type dopability, ultrawide bandgap, and high critical field. Optimization of crystal growth processes to promote beneficial defects and suppress harmful ones requires accurate quantitative modelling of both native and impurity defects. Herein we quantitatively model defect concentrations as a function of bulk crystal growth conditions and demonstrate the necessity of including effects such as bandgap temperature dependence, chemical potentials from thermochemistry, and defect vibrational entropy in modelling based on defect formation energies computed by density functional theory (DFT) with hybrid functionals. Without these contributions, grossly-erroneous and misleading predictions arise, e.g. that n-type doping attempts would be fully compensated by Ga vacancies. Including these effects reproduces the experimental facts that melt-grown Sn-doped β-Ga2O3 crystals are conductive with small compensation while annealing the same crystals in O2 at intermediate temperatures renders them insulating. To accomplish this modeling, we developed a comprehensive modelling framework (KROGER) based on calculated defect formation energies and flexible thermodynamic conditions. These capabilities allow KROGER to capture full and partial defect equilibria amongst native defects and impurities occurring during specific semiconductor growth or fabrication processes. We use KROGER to model 873 charge-states of 259 defects involving 19 elements in conditions representing bulk crystal growth by edge-fed growth (EFG) and annealing in oxygen. Our methodology is transferrable to a wide range of materials beyond β-Ga2O3. The integration of thermodynamic and first-principles modelling of point defects provides insight into optimization of point defect populations in growth and processing. Copyright © 2025, The Authors. All rights reserved.

关键词： Point defects

Memristor Compact Model with Oxygen-Vacancy Concentration as State Variable

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arXiv 2022年

作者： Zeumault, Andre Alam, Shamiul Faruk, Md. Omar Aziz, Ahmedullah Department of Electrical Engineering and Computer Science The University of Tennessee KnoxvilleTN37996 United States Department of Materials Science and Engineering University of Tennessee KnoxvilleTN37996 United States

We present a unique compact model for oxide memristors, based upon the concentration of oxygen vacancies as state variables. In this model, the increase (decrease) in oxygen vacancy concentration is similar in effect to the reduction (expansion) of the tunnel gap used as a state variable in existing compact models, providing a mechanism for the electronic current to increase (decrease) based upon the polarity of the applied voltage. Rate equations defining the dynamics of state variables are obtained from simplifications of a recent manuscript in which electronic processes (i.e., electron capture/emission) were combined with atomic processes (i.e., Frenkel pair generation/recombination, diffusion) stemming from the thermochemical model of dielectric breakdown. Central to the proposed model is the effect of the electron occupancy of oxygen vacancy traps on resistive switching dynamics. The electronic current is calculated considering Ohmic, band-to-band, and bound-to-band contributions. The model includes uniform self-heating with Joule-heating and conductive loss terms. The model is calibrated using experimental current-voltage characteristics for HfO2 memristors with different electrode materials. Though a general model is presented, a delta-shaped density of states profile for oxygen vacancies is found capable of accurately representing experimental data while providing a minimal description of bound to band transitions. The model is implemented in Verilog-A and tested using read/write operations in a 4x4 1T1R nonvolatile memory array to evaluate its ability to perform circuit simulations of practical interest. A particular benefit is that the model does not make strong assumptions regarding filament geometry of which scant experimental-evidence exists to support. © 2022, CC BY.

关键词： Memristors

Passive frequency-conversion imaging from the near-infrared to the visible

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Passive frequency-conversion imaging from the near-infrared ...

Conference on Lasers and Electro-Optics (CLEO)

作者： Demeng Feng Rabeeya Hamid Emma Belliveau Manchen Hu Pournima Narayanan Jad Salman Chenghao Wan Bryan E. Rubio-Perez Daniel N. Congreve Mikhail A. Kats Department of Electrical and Computer Engineering University of Wisconsin-Madison Madison WI USA Department of Electrical Engineering Stanford University Stanford CA USA Department of Chemistry Stanford University Stanford CA USA Department of Materials Science and Engineering University of Wisconsin-Madison Madison WI USA Department of Physics University of Wisconsin-Madison Madison WI USA

We demonstrate a passive frequency-conversion imaging system that converts near-infrared images into visible images, enabling near-infrared imaging with the naked eye or a conventional visible camera.

ISBN: (纸本)9781957171258

关键词： Diode lasers Image quality Near infrared radiation Quantum efficiency Ultraviolet radiation Visible light

Synthetic Batik Pattern Generator Using Wasserstein Generative Adversarial Network with Gradient Penalty

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Synthetic Batik Pattern Generator Using Wasserstein Generati...

International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)

作者： Kus Andriadi Yaya Heryadi Lukas Wayan Suparta Ilvico Sonata Computer Science Department Binus Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Cognitive Engineering Research Group (CERG) Universitas Katolik Indonesia Atma Jaya Jakarta Indonesia Department of Electrical Engineering Faculty of Industrial Technology Institut Teknologi Nasional Yogyakarta Yogyakarta Indonesia

Batik is an Indonesian world cultural heritage. Batik consists of many kinds of patterns depending on where the batik comes from, Batik-making techniques continue to develop along with technology development. Among the batik making techniques that are widely used are hand-written, stamping, and printing. Batik motifs have been widely used as research material, especially in the field of artificial intelligence. The diverse appearance of batik motifs has attracted many researchers to carry out research on making synthetic batik patterns, one of which uses a Generative Adversarial Network. This paper presents a synthetic batik pattern model based on the Wasserstein Generative Adversarial Network with Gradient Penalty. This model has been proven to create new synthetic batik patterns quite well and almost identical with images provided in the dataset, with the notes if the dataset provided is large.

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Linking Molecular Origin of Melt Fragility Index with Topological Phases of Network Glasses

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SSRN

SSRN 2023年

作者： Gogi, Vamshi Kiran Mandal, Avik Welton, Aaron Mohanty, Chandi Bhosle, Siddhesh Chakraborty, Shibalik Gunasekera, Kapila Chakravarty, Soumendu Almutairi, Badriah Boolchand, Punit Department of Electrical Engineering and Computer Science University of Cincinnati CincinnatiOH45221-0030 United States Department of Mechanical and Materials Engineering University of Cincinnati CincinnatiOH United States Department of Physics University of Cincinnati CincinnatiOH United States

Network glasses are composed of three topological phases: flexible, intermediate, and stressed-rigid. Intermediate Phase (IP) glasses form compact, rigid, and stress-free networks with no Open Degrees of Freedom (ODF). IP melts are observed to be super-strong with the lowest fragility index, m = 15 due to the absence of ODF in the parent glass. This feature is general and observed in multiple selenide, sulfide, and modified oxide glasses can be traced to Isostatically Rigid Local Structures (ISRLSs) formed in the IP. On the other hand, the flexible and stressed-rigid phase glasses form non-compacted and stressed networks with increasing residual pressure as the count of ODF increases. Their melts are found to be fragile and display fragility indices m > 20 as the count of the ODF in the glass increases and the count of ISRLSs dissipates. © 2023, The Authors. All rights reserved.

关键词： Degrees of freedom (mechanics)

On the Impact of Knowledge Distillation for Model Interpretability

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arXiv 2023年

作者： Han, Hyeongrok Kim, Siwon Choi, Hyun-Soo Yoon, Sungroh Department of Electrical and Computer Engineering Seoul National University Seoul Korea Republic of Department of Computer Science and Engineering Seoul National University of Science and Technology Seoul Korea Republic of ZIOVISION Inc. Chuncheon Korea Republic of Interdisciplinary Program in Artificial Intelligence Seoul National University Seoul Korea Republic of

Several recent studies have elucidated why knowledge distillation (KD) improves model performance. However, few have researched the other advantages of KD in addition to its improving model performance. In this study, we have attempted to show that KD enhances the interpretability as well as the accuracy of models. We measured the number of concept detectors identified in network dissection for a quantitative comparison of model interpretability. We attributed the improvement in interpretability to the class-similarity information transferred from the teacher to student models. First, we confirmed the transfer of class-similarity information from the teacher to student model via logit distillation. Then, we analyzed how class-similarity information affects model interpretability in terms of its presence or absence and degree of similarity information. We conducted various quantitative and qualitative experiments and examined the results on different datasets, different KD methods, and according to different measures of interpretability. Our research showed that KD models by large models could be used more reliably in various fields. © 2023, CC BY-NC-SA.

关键词： Distillation