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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE *** this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related *** order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB *** rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion Conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

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High Resolution of City-Level Climate Simulation by GPU with Multi-physical Phenomena 18th

High Resolution of City-Level Climate Simulation by GPU with...

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18th IFIP WG 10.3 International Conference on Network and Parallel Computing, NPC 2021

作者： Watanabe, Koei Kikuchi, Kohei Boku, Taisuke Sato, Takuto Kusaka, Hiroyuki Master’s Program in Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukubashi Japan Center for Computational Sciences University of Tsukuba Tsukubashi Tennodi Japan

ISBN: (纸本)9783030935702

In this paper, we describe the Graphics Processing Unit (GPU) implementation of our City-LES code on detailed large eddy simulations, including the multi-physical phenomena on fluid dynamics, heat absorption and reflection by surface and building materials, cloud effects, and even sunlight effect. Because a detailed simulation involving these phenomena is required for analyses at the street level and several meters of resolution, the computation amount is enormous, and ordinary CPU computation cannot provide sufficient performance. Therefore, we implemented the entire code on GPU clusters with large-scale computing. We applied OpenACC coding to incrementally implement relatively easy programming and eliminate data transfers between the CPU and GPU memories. Based on this research, we determined that the elimination of data transfers is effective, even in the case where a part of the code execution on the GPU is slower than the CPU, owing to the absence of spatial parallelism. The objective of this study is to perform a complete climate simulation on a few square-kilometers field around the Tokyo Station, considering the finest resolution of the original highlighted area of the Marathon race in the Olympic Games Tokyo 2020. We successfully transferred the entire code to the GPU to provide approximately eight times the performance of CPU-only computation on multi-GPU per node with a large scale cluster. © 2022, IFIP International Federation for Information Processing.

关键词： Graphics processing unit

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Experiences in teaching and mentoring interdisciplinary graduate students of diversified backgrounds

Experiences in teaching and mentoring interdisciplinary grad...

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2008 ASEE Annual Conference and Exposition

作者： Mohan, Ram Kelkar, Vinaya Kelkar, Ajit North Carolina AandT State University Department of Computational Science and Engineering Graduate Program North Carolina AandT State University Department of Biology North Carolina AandT State University

The interdisciplinary master's degree program in computational science and Engineering (CSE) at North Carolina A&T State University, Greensboro, NC is now more than 3 years old, and provides graduate education in several computational areas and the associated primary field disciplines. The CSE program since its inception has presently graduated more than 12 students who are currently placed in several major industries. Our CSE graduate program offers an interdisciplinary curriculum combining computational core areas along with various domain areas. The students enrolled in the program begin with diversified backgrounds (prior undergraduate studies in various fields such as engineering, physical sciences, life sciences, mathematics, business, etc), and are required to take four core courses relevant to CSE for their graduation in the areas of applied probability and statistics, comprehensive numerical analysis, Data structures and parallel programming, computational and scientific visualization irrespective of their prior background. The preparation level for the diversified group of students in these courses depends on their undergraduate major. This poses significant challenges to graduate faculty teaching these courses and mentoring these students with diversified backgrounds. Our experiences and observations with the course content and structure, teaching methods, evaluation and student performances in these courses with diversified graduate students and their mentoring for the past 3 years are presented. The performances of the students in these core courses are correlated to their background and analyzed. Our experiences indicate students with a lesser preparation level seem to get geared quickly via peer guidance from the stronger students. In several cases, the performances were not related to an individual's prior background, but on their motivation and willingness to strive and succeed. The experiences indicate that the students can benefit well with additi

关键词： Students

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Novelty-based incremental document clustering for on-line documents 22

Novelty-based incremental document clustering for on-line do...

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22nd International Conference on Data Engineering Workshops, ICDEW 2006

作者： Khy, Sophoin Ishikawa, Yoshiharu Kitagawa, Hiroyuki Master's Program in Science and Engineering Tsukuba Ibaraki Japan Graduate School of Systems and Information Engineering Tsukuba Ibaraki Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki Japan

ISBN: (纸本)0769525717

Document clustering has been used as a core technique in managing vast amount of data and providing needed information. In on-line environments, generally new information gains more interests than old one. Traditional clustering focuses on grouping similar documents into clusters by treating each document with equal weight. We proposed a novelty-based incremental clustering method for on-line documents that has biases on recent documents. In the clustering method, the notion of 'novelty' is incorporated into a similarity function and a clustering method, a variant of the K-means method, is proposed. We examine the efficiency and behaviors of the method by experiments. © 2006 IEEE.

关键词： Cluster analysis

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Machine learning based prediction of cognitive metrics using major biomarkers in SuperAgers

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Scientific Reports 2025年第1期15卷 1-20页

作者： Hyo-Bin Lee Jang-Hwan Choi So-Yeon Kwon Ji-Hae Park Young Mi Park Bori Kim Geon-Ha Kim Department of Computational Medicine Graduate Program in System Health Science and Engineering Ewha Womans University Seoul 07804 Korea Department of Artificial Intelligence Ewha Womans University Seoul 03760 Korea Department of Molecular Medicine Ewha Womans University Seoul 07804 Korea Department of Neurology Ewha Womans University Mokdong Hospital Ewha Womans University Seoul 07985 Korea

As populations age, understanding cognitive decline and age-related diseases like dementia has become increasingly important. “SuperAgers,” individuals over 65 with cognitive abilities similar to those in their 40s, provide a unique perspective on cognitive reserve. This study analyzed 55 blood biomarkers, including cellular components and metabolism/inflammation-related factors, in 39 SuperAgers and 42 typical agers. While conventional statistical analyses identified significant differences in only four biomarkers, advanced feature selection and machine learning techniques revealed a broader set of 15 key biomarkers associated with SuperAger status. A predictive model built using these biomarkers achieved an accuracy of 76% in cognitive domain prediction. To address the limitation of small sample sizes, data augmentation leveraging large language models improved the model’s robustness. Shapley Additive exPlanations (SHAP) provided interpretability, revealing the impact of specific blood factors on cognitive function. These findings suggest that certain blood biomarkers are not only associated with cognitive performance but may also serve as indicators of cognitive reserve. By utilizing simple blood tests, this research presents a clinically significant method for predicting cognitive function and identifying SuperAger status in healthy elderly individuals, offering a foundation for future studies on the biological mechanisms underpinning cognitive resilience.

关键词： BORUTA Blood biomarkers Cognitive decline Cognitive function Cognitive metric prediction Machine learning Recursive feature elimination (RFE) Super-Agers

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An information theoretic framework for eukaryotic gradient sensing 19

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20th Annual Conference on Neural Information Processing Systems, NIPS 2006

作者： Kimmel, Joseph M. Salter, Richard M. Thomas, Peter J. Computer Science Program Oberlin College Oberlin OH 44074 United States Department of Mathematics Biology and Cognitive Science Case Western Reserve University Cleveland OH 44106 United States Computational Neuroscience Graduate Program University of Chicago United States Center for Computation and Modeling United States

ISBN: (纸本)9780262195683

Chemical reaction networks by which individual cells gather and process information about their chemical environments have been dubbed "signal transduction" networks. Despite this suggestive terminology, there have been few attempts to analyze chemical signaling systems with the quantitative tools of information theory. Gradient sensing in the social amoeba Dictyostelium discoideum is a well characterized signal transduction system in which a cell estimates the direction of a source of diffusing chemoattractant molecules based on the spatiotemporal sequence of ligand-receptor binding events at the cell membrane. Using Monte Carlo techniques (MCell) we construct a simulation in which a collection of individual ligand particles undergoing Brownian diffusion in a three-dimensional volume interact with receptors on the surface of a static amoeboid cell. Adapting a method for estimation of spike train entropies described by Victor (originally due to Kozachenko and Leonenko), we estimate lower bounds on the mutual information between the transmitted signal (direction of ligand source) and the received signal (spatiotemporal pattern of receptor binding/unbinding events). Hence we provide a quantitative framework for addressing the question: how much could the cell know, and when could it know it? We show that the time course of the mutual information between the cell's surface receptors and the (unknown) gradient direction is consistent with experimentally measured cellular response times. We find that the acquisition of directional information depends strongly on the time constant at which the intracellular response is filtered.

关键词： Ligands

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Modelling of Motion of a Volvox Colony using Many-Body System and Its Qualitative Comparison with Observations 9

Modelling of Motion of a Volvox Colony using Many-Body Syste...

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9th Asian Physics Symposium 2021, APS 2021

作者： Dini, Septian Ulan Nurafni, Sevi Fairuza, Achmad Zacky Taufik, Intan Master Program in Physics Faculty of Mathematics and Natural Science InstitutTeknologi Bandung Bandung40132 Indonesia Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Bandung40132 Indonesia Master Program in Nanotechnology Graduate School Institut Teknologi Bandung Bandung40132 Indonesia School of Life Science and Technology Institut Teknologi Bandung40132 Indonesia

Approximately 500-60,000 volvox cells constructed a colony with a spherical or elliptical hollow form. Each cell can use its flagella to move. For a colony of hundred cells to perform a direct motion, there must be a coordination of the flagella. In this work, we assume that the cells already form the spherical colony and can perform some simple motion types, i.e., translational (TRAN), roll (ROLL), spin (SPIN), and superposition of the motions, and neglect detail of each flagellum. It is possible to map each cell in the colony using angular positions with a constant radius R and different θ _i and φ_i, where i = 1, 2,..., N with N is the number of cells constructing a colony. The center of the colony is R = (x, y, z). The TRAN mode can be obtained, wherex(t) = x(0) + vxt, y(t) = y(0) + vyt, z(t) = z(0) +vzt, ROLLmode with θ(t) = ω(0) + ωθt and SPIN with φ(t) = ω(0) + ωφt. Through the available observation video, the model of volvox colony motion is also shown to have a qualitative agreement. © Published under licence by IOP Publishing Ltd.

关键词： Cells

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Confined VLS Growth of Single-Layer 2D Tungsten Nitrides

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ACS Applied Materials and Interfaces 2024年第1期16卷 1705-1711页

作者： Chin, Hao-Ting Wang, Deng-Chi Wang, Hao Muthu, Jeyavelan Khurshid, Farheen Chen, Ding-Rui Hofmann, Mario Chuang, Feng-Chuan Hsieh, Ya-Ping Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei 106 Taiwan International Graduate Program of Molecular Science and Technology National Taiwan University Taipei 10617 Taiwan Institute of Atomic and Molecular Sciences Academia Sinica Taipei 106 Taiwan Department of Physics National Sun Yat-Sen University Kaohsiung 80424 Taiwan Department of Physics National Taiwan University Taipei 106 Taiwan Nano Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei 106 Taiwan Center for Theoretical and Computational Physics National Sun Yat-sen University Kaohsiung 80424 Taiwan Physics Division National Center for Theoretical Sciences Taipei 10617 Taiwan

Two-dimensional (2D) metal nitrides have garnered significant interest due to their potential applications in future electronics and quantum systems. However, the synthesis of such materials with sufficient uniformity and at relevant scales remains an unaddressed challenge. This study demonstrates the potential of confined growth to control and enhance the morphology of 2D metal nitrides. By restricting the reaction volume of vapor-liquid-solid reactions, an enhanced precursor concentration was achieved that reduces the nucleation density, resulting in larger grain sizes and suppression of multilayer growth. Detailed characterization reveals the importance of balancing the energetic and kinetic aspects of tungsten nitride formation toward this ability. The introduction of a promoter enabled the realization of large-scale, single-layer tungsten nitride with a uniform and high interfacial quality. Finally, our advance in morphology control was applied to the production of edge-enriched 2D tungsten nitrides with significantly enhanced hydrogen evolution ability, as indicated by an unprecedented Tafel slope of 55 mV/dec. © 2023 American Chemical Society.

关键词： 2D diode confinement growth HER promoter-assisted growth tungsten nitride VLS

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Interannual variability and climatic sensitivity of global wildfire activity

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Advances in Climate Change Research 2021年第5期12卷 686-695页

作者： Rongyun TANG Jiafu MAO Mingzhou JIN Anping CHEN Yan YU Xiaoying SHI Yulong ZHANG Forrest M.HOFFMAN Min XU Yaoping WANG Institute for a Secure and Sustainable Environment University of TennesseeKnoxville37996USA Environmental Sciences Division and Climate Change Science Institute Oak Ridge National LaboratoryOak Ridge37830USA Department of Biology and Graduate Degree Program in Ecology Colorado State UniversityFort Collins80523USA Atmospheric and Oceanic Sciences Program Princeton UniversityPrinceton08544USA Computational Sciences and Engineering Division and Climate Change Science Institute Oak Ridge National LaboratoryOak Ridge37830USA

Understanding historical wildfire variations and their environmental driving mechanisms is key to predicting and mitigating wildfires. However, current knowledge of climatic responses and regional contributions to the interannual variability (IAV) of global burned area remains limited. Using recent satellite-derived wildfire products and simulations from version v1.0 of the land component of the U.S. Department of Energy's Energy Exascale Earth System Model (E3SM land model [ELM] v1) driven by three different climate forcings, we investigated the burned area IAV and its climatic sensitivity globally and across nine biomes from 1997 to 2018. We found that 1) the ELM simulations generally agreed with the satellite observations in terms of the burned area IAV magnitudes, regional contributions, and covariations with climate factors, confirming the robustness of the ELM to the usage of different climate forcing sources;2) tropical savannas, tropical forests, and semi-arid grasslands near deserts were primary contributors to the global burned area IAV, collectively accounting for 71.7%–99.7% of the global wildfire IAV estimated by both the satellite observations and ELM simulations;3) precipitation was a major fire suppressing factor and dominated the global and regional burned area IAVs, and temperature and shortwave solar radiation were mostly positively related with burned area IAVs;and 4) noticeable local discrepancies between the ELM and remote-sensing results occurred in semi-arid grasslands, croplands, boreal forests, and wetlands, likely caused by uncertainties in the current ELM fire scheme and the imperfectly derived satellite observations. Our findings revealed the spatiotemporal diversity of wildfire variations, regional contributions and climatic responses, and provided new metrics for wildfire modeling, facilitating the wildfire prediction and management.

关键词： Wildfire Burned area Climatic sensitivity E3SM land model Global fire emission database

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Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals

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Cell 2025年第10期188卷 2794-2809.e21页

作者： Mi, Xuelong Chen, Alex Bo-Yuan Duarte, Daniela Carey, Erin Taylor, Charlotte R. Braaker, Philipp N. Bright, Mark Almeida, Rafael G. Lim, Jing-Xuan Ruetten, Virginia M.S. Wang, Yizhi Wang, Mengfan Zhang, Weizhan Zheng, Wei Reitman, Michael E. Huang, Yongkang Wang, Xiaoyu Li, Lei Deng, HanFei Shi, Song-Hai Poskanzer, Kira E. Lyons, David A. Nimmerjahn, Axel Ahrens, Misha B. Yu, Guoqiang Bradley Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington 22203 VA United States Janelia Research Campus Howard Hughes Medical Institute Ashburn 20147 VA United States Department of Molecular and Cellular Biology Harvard University Cambridge 02138 MA United States Graduate Program in Neuroscience Harvard Medical School Boston 02115 MA United States Waitt Advanced Biophotonics Center The Salk Institute for Biological Studies La Jolla 92037 CA United States Department of Biochemistry & Biophysics University of California San Francisco San Francisco CA United States Neuroscience Graduate Program University of California San Francisco San Francisco CA United States Centre for Discovery Brain Sciences University of Edinburgh Edinburgh BioQuarter Edinburgh EH16 4SB United Kingdom Gatsby Computational Neuroscience Unit UCL London W1T 4JG United Kingdom Kavli Institute for Fundamental Neuroscience San Francisco CA United States Department of Automation Tsinghua University Beijing 100084 China IDG/McGovern Institute for Brain Research Tsinghua University Beijing 100084 China New Cornerstone Science Laboratory Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Beijing 100084 China State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Institutes of Brain Science Fudan University Shanghai 200032 China Beijing National Research Center for Information Science and Technology Beijing 100084 China

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord. © 2025 The Author(s)

关键词： AQuA2 astrocytes cell interaction analysis functional units glial cells image analysis machine learning molecular spatiotemporal signals neurons time-lapse imaging

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