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A computational information criterion for particle-tracking with sparse or noisy data

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arXiv 2021年

作者： Tran, Nhat Thanh Benson, David A. Schmidt, Michael J. Pankavich, Stephen D. Department of Mathematics University of California Irvine IrvineCA92697 United States Hydrologic Science and Engineering Program Department of Geology and Geological Engineering Colorado School of Mines GoldenCO80401 United States Center for Computing Research Sandia National Laboratories AlbuquerqueNM87185 United States Department of Applied Mathematics and Statistics Colorado School of Mines GoldenCO80401 United States

Traditional probabilistic methods for the simulation of advection-diffusion equations (ADEs) often overlook the entropic contribution of the discretization, e.g., the number of particles, within associated numerical methods. Many times, the gain in accuracy of a highly discretized numerical model is outweighed by its associated computational costs or the noise within the data. We address the question of how many particles are needed in a simulation to best approximate and estimate parameters in one-dimensional advective-diffusive transport. To do so, we use the well-known Akaike Information Criterion (AIC) and a recently-developed correction called the Computational Information Criterion (COMIC) to guide the model selection process. Random-walk and mass-transfer particle tracking methods are employed to solve the model equations at various levels of discretization. Numerical results demonstrate that the COMIC provides an optimal number of particles that can describe a more efficient model in terms of parameter estimation and model prediction compared to the model selected by the AIC even when the data is sparse or noisy, the sampling volume is not uniform throughout the physical domain, or the error distribution of the data is non-IID Gaussian. Keywords: Computational Information Criterion, Lagrangian Modeling, Particle Methods, Diffusion-reaction Equation, Non-Gaussian Error Distribution Copyright © 2021, The Authors. All rights reserved.

关键词： Advection

Electrochemical detection of antimalarial drug (Amodiaquine) using Dy-MOF@MWCNTs composites to prevent erythrocytic stages of plasmodium species in human bodies

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Microchemical Journal 2024年 202卷

作者： Peter, X. Thatheyus Kuo, Chih-Yu Malar, P. Govindasamy, Mani Rajaji, Umamaheswari Yusuf, Kareem Thinfilm Photovoltaics Laboratory Department of Physics and Nanotechnology SRM Institute of Science and Technology Tamil Nadu Kattankulathur 603203 India Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City 243303 Taiwan Research Center for Intelligence Medical Devices Ming Chi University of Technology New Taipei City 243303 Taiwan Centre for Applied Research Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences (SIMATS) Tamil Nadu Chennai 602105 India Department of Chemistry College of Science King Saud University Riyadh 11451 Saudi Arabia

Herein, we report on fabrication of dysprosium-based metal–organic framework (Dy-MOF)@multiwalled carbon nanotubes (MWCNT) composites modified with glassy carbon electrode (Dy-MOF@MWCNT/GC) as a working electrode for Antimalarial drug detection. Dy-MOF@MWCNT composites was prepared by sonochemical process along with ultrasonication. The composite structure, phase purity, morphology and composition of the composites were confirmed by X-ray diffraction, Scanning electron microscope, and X-ray photoelectron spectroscopy. Further, Dy@MWCNT composites were deposited on a glassy carbon electrode by drop casting method, and used as an electrode material to efficiently detect Amodiaquine (ADD) by electrochemical techniques such as CV and DPV. The as-prepared Dy@MWCNT composite material showed the oxidation peak current of ADD to be ∼ 60 % higher than other unmodified GC electrodes and showed a low charge transfer resistance (R_ct) of 24 Ω. The Dy@MWCNT provided a broad linear range of 0.4 to 20 µM with a limit of detection of 0.377 μM and sensitivity of 1.817 μA.μM⁻¹ for the detection of ADD. According to the pH study, the amount of electrons and protons involved in the electrochemical processes of ADD was calculated and a plausible mechanism for ADD electro-oxidation was proposed. Thus, the prepared sensor exhibited practical usefulness by determining the ADD drug in human urine samples. Hence, the results shows that the Dy@MWCNT- modified sensor has good electrocatalytic activity for the redox of ADD. © 2024 Elsevier B.V.

关键词： Amodiaquine Antimalarial drug Carbon nanomaterials Electrochemical sensor Metal organic framework

Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC 29th

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Decoding the Functional Interactome of Non-model Organisms...

29th International Conference on Research in Computational Molecular Biology, RECOMB 2025

作者： Sledzieski, Sam Versavel, Charlotte Singh, Rohit Ocitti, Faith Devkota, Kapil Kumar, Lokender Shpilker, Polina Roger, Liza Yang, Jinkyu Lewinski, Nastassja Putnam, Hollie Berger, Bonnie Klein-Seetharaman, Judith Cowen, Lenore Center for Computational Biology Flatiron Institute New YorkNY United States Department of Computer Science Tufts University MedfordMA United States Departments of Biostatistics and Bioinformatics Duke University DurhamNC United States School of Biotechnology Faculty of Applied Sciences and Biotechnology Shoolini University Himachal Pradesh Solan173229 India School of Molecular Sciences and School of Ocean Futures Arizona State University TempeAZ United States Department of Mechanical Engineering Seoul National University Seoul Korea Republic of Department of Chemical and Life Science Engineering Virginia Commonwealth University RichmondVA United States Department of Biological Sciences University of Rhode Island KingstonRI United States Computer Science and Artificial Intelligence Laboratory and Department of Mathematics MIT CambridgeMA United States School of Molecular Sciences and College of Health Solutions Arizona State University PhoenixAZ United States

ISBN: (纸本)9783031902512

We introduce PHILHARMONIC, a computational framework that couples deep learning de novo network inference with robust unsupervised spectral clustering algorithms to uncover functional relationships and high-level organization in non-model organisms. Our novel clustering approach produces highly informative functional modules by de-noising the predicted network. We also develop a novel algorithm called ReCIPE, which aims to reconnect disconnected clusters, increasing functional enrichment and biological interpretability. We initially perform remote homology-based functional annotation by leveraging hmmscan and GODomainMiner to assign initial functions to proteins at large evolutionary distances;our clusters then enable us to newly assign functions to uncharacterized proteins through "function by association." We validate the ability of PHILHARMONIC to recover gold-standard functional enrichments in the well-annotated fruit fly D. melanogaster, and apply it to investigate stress response in the reef-building coral P. damicornis and its algal symbiont C. goreaui. Easy to run end-to-end and requiring only a sequenced proteome, PHILHARMONIC is an engine for biological hypothesis generation and discovery in non-model organisms. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Deep learning

Crafting the future: Enhancing gas separation with nanoarchitectonics of bimetallic Ni–Co-ZIF-67 in polysulfone-based mixed matrix membranes

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Case Studies in chemical and Environmental engineering 2024年 9卷

作者： Sulistiono, Dety Oktavia Ali, Badrut Tamam Ibnu Widyanto, Alvin Rahmad Ediati, Ratna Widiastuti, Nurul Lestari, Witri Wahyu Akhlus, Syafsir Iqbal, Rendy Muhamad Senda, Semuel Pati Fansuri, Hamzah Department of Chemistry Faculty of Science and Data Analytics Institut Teknologi Sepuluh Nopember Sukolilo Surabaya 60111 Indonesia Automotive Engineering Engineering Department Politeknik Negeri Jember Jember 68101 Indonesia Center for Process and Manufacturing Industry Technology National Research and Innovation Agency Technology Energy Cluster PUSPIPTEK 625 Building South Tangerang Indonesia Department of Applied Chemistry Shibaura Institute of Technology 3-7-5 Toyosu Koto-ku Tokyo 135-8548 Japan Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Sebelas Maret Jl. Ir. Sutami No. 36A Kentingan Jebres Surakarta 57126 Indonesia Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Palangka Raya Kampus UPR Tunjung Nyaho Palangkaraya 73111 Indonesia Advanced Membrane Technology Research Center (AMTEC) Faculty of Chemical and Energy Engineering Universiti Teknologi Malaysia Johor Skudai 81310 Malaysia

In response to global clean energy demands, this study develops mixed matrix membranes (MMMs) for gas separation in renewable energy applications. MMMs are produced through phase inversion by employing polysulfone and bimetallic-ZIF (Ni–Co-ZIF-67). Bimetallic-ZIF, formed in-situ by Co and Ni metals in water solvent with triethylamine, enhances gas selectivity. MMMs with 4 wt% bimetallic-ZIF, Co: Ni ratio of 9:1 (4Ni10Z67), exhibit remarkable selectivity: CO₂/CH₄ (21.19), H₂/N₂ (1.47), H₂/CH₄ (44.82), and N₂/CH₄ (30.40). Strong interactions between bimetallic-ZIF and CO₂, facilitated by molecular sieving and Ni–Co sites, contribute to these results. © 2024 The Authors

关键词： Bimetallic-ZIF CO2 capture Gas emissions Metal substitution Renewable energy

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

Incremental learning and state-space evolving fuzzy control of nonlinear time-varying systems with unknown model

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arXiv 2021年

作者： Leite, Daniel Coutinho, Pedro Bessa, Iury Camargos, Murilo Cordovil Junior, Luiz A.Q. Palhares, Reinaldo Department of Automatics Federal University of Lavras Brazil Graduate Program in Electrical Engineering Federal University of Minas Gerais Brazil Department of Electricity Federal University of Amazonas Brazil School of Applied Mathematics Fundação Getulio Vargas Rio de Janeiro Brazil Department of Electronics Engineering Federal University of Minas Gerais Brazil

We present a method for incremental modeling and time-varying control of unknown nonlinear systems. The method combines elements of evolving intelligence, granular machine learning, and multi-variable control. We propose a State-Space Fuzzy-set-Based evolving Modeling (SS-FBeM) approach. The resulting fuzzy model is structurally and parametrically developed from a data stream with focus on memory and data coverage. The fuzzy controller also evolves, based on the data instances and fuzzy model parameters. Its local gains are redesigned in real-time – whenever the corresponding local fuzzy models change – from the solution of a linear matrix inequality problem derived from a fuzzy Lyapunov function and bounded input conditions. We have shown one-step prediction and asymptotic stabilization of the Henon chaos. © 2021, CC BY-NC-SA.

关键词： Fuzzy control

Computational Design of Anisotropic Stealthy Hyperuniform Composites with Engineered Directional Scattering Properties

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arXiv 2023年

作者： Shi, Wenlong Keeney, David Chen, Duyu Jiao, Yang Torquato, Salvatore Materials Science and Engineering Arizona State University TempeAZ85287 United States Materials Research Laboratory University of California Santa BarbaraCA93106 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Disordered hyperuniform materials are an emerging class of exotic amorphous states of matter that endow them with singular physical properties, including large isotropic photonic band gaps, superior resistance to fracture, and nearly optimal electrical and thermal transport properties, to name but a few. Here, we generalize the Fourier-space based numerical construction procedure for designing and generating digital realizations of isotropic disordered hyperuniform two-phase heterogeneous materials (i.e., composites) developed by Chen and Torquato [Acta Mater. 142, 152 (2018)] to anisotropic microstructures with targeted spectral densities. Our generalized construction procedure explicitly incorporates the vector-dependent spectral density function χ˜V (k) of arbitrary form that is realizable. We demonstrate the utility of the procedure by generating a wide spectrum of anisotropic stealthy hyperuniform (SHU) microstructures with χ˜V (k) = 0 for k ∈ Ω, i.e., complete suppression of scattering in an "exclusion" region Ω around the origin in the Fourier space. We show how different exclusion-region shapes with various discrete symmetries, including circular-disk, elliptical-disk, square, rectangular, butterfly-shaped and lemniscate-shaped regions of varying size, affect the resulting statistically anisotropic microstructures as a function of the and phase volume fraction. The latter two cases of Ω lead to directionally hyperuniform composites, which are stealthy hyperuniform only along certain directions, and are non-hyperuniform along others. We find that, while the circular-disk exclusion regions give rise to isotropic hyperuniform composite microstructures, the directional hyperuniform behaviors imposed by the shape asymmetry (or anisotropy) of certain exclusion regions give rise to distinct anisotropic structures and degree of uniformity in the distribution of the phases on intermediate and large length scales along different directions. Moreover, while the anisotr

关键词： Volume fraction

SNP (A > G - rs13057211) but not GT(n) polymorphism in HMOX-1 promotor gene is associated with COVID-19 mortality

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BMC Pulmonary Medicine 2023年第1期23卷 514-514页

作者： Fares, Kerolos El-Deeb, Mona K. Elsammak, Omar Ouf, Amged Saeed, Hesham Mahmoud Sayd Baess, Ayman Elsammak, Mohamed El-Attar, Eman Department of Chemical Pathology Medical Research Institute Alexandria University Alexandria Egypt Department of Clinical Laboratory Sciences College of Applied Medical Sciences Al Jouf University Sakakah Saudi Arabia Faculty of Medicine Alexandria University Alexandria Egypt Department of Biology and Biotechnology Graduate Program School of Sciences and Engineering (SSE) The American University in Cairo (AUC) New Cairo Egypt Department of Biotechnology Institute of Graduate Studies and Research Alexandria University Alexandria Egypt Department of Chest Diseases Faculty of Medicine Alexandria University Alexandria Egypt

Introduction: COVID-19 causes severe inflammatory respiratory distress syndrome. The global pandemic caused millions of cases of morbidity and mortality worldwide. Patients may present with variable symptoms including dyspnea, fever, and GIT manifestations. The HMOX-1 gene is located on the long (q) arm of chromosome 22 at position 12.3. HMOX-1 is expressed in all mammalian tissues at basal levels and is considered as a stress response enzyme. HMOX-1 has a specific polymorphic site with variable GT(n) repeats at the promotor region. Several authors evaluated the HMOX-1 GT(n) promoter polymorphism in different inflammatory conditions. We evaluated HMOX-1 promoter polymorphism in relation to serum Hemoxygenase level and inflammatory makers (CRP, Ferritin, PCT, IL-6 and D-dimer) in patients affected by SARS-COV-2 disease. Subjects and methods: Ninety patients confirmed to be infected with COVID-19 were followed up till the study end point (recovery and discharge or death). HMOX-1 promotor GT(n) polymorphism was evaluated using Sanger sequencing. HMOX-1 enzyme serum level was measured by ELISA and the level of different inflammatory markers was assessed by available commercial kits. Results: A novel Single nucleotide polymorphism (SNP) (A > G) - rs13057211 in the GT(n) region of HMOX-1 promoter gene was found in 40 (61.5%) COVID-19 patients out of the studied 65 patients. This (A > G) SNP was associated with higher mortality rate in COVID-19 as it was detected in 27 patients (75% of the patients who succumbed to the disease) (p = 0.021, Odds ratio = 3.7;95% CI:1.29–10.56). Serum IL-6 (Interleuken-6) was positively correlated the length of Hospital Stay (LOHS) and procalcitonin (PCT);(p = 0.014, r: 0.651 and p < 0.001, r:0.997) respectively while negatively correlated with levels of HMOX-1 enzyme serum level (p = 0.013, r: -0.61). CRP correlated positively with LOHS (p = 0.021, r = 0.4), PCT (p = 0.044, r = 0.425) and age (p < 0.001, r = 0.685). Higher levels of D-Dimer

关键词： COVID-19 IL-6 Promoter GT(n) polymorphism Serum Hemoxygenase-1 SNP

Applications of mean field games in financial engineering and economic theory

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arXiv 2020年

作者： Carmona, René DEPARTMENT OF OPERATIONS RESEARCH & FINANCIAL ENGINEERING BENDHEIM CENTER FOR FINANCE PROGRAM IN APPLIED & COMPUTATIONAL MATHEMATICS PRINCETON UNIVERSITY United States

This is an expanded version of the lecture given at the AMS Short Course on Mean Field Games, on January 13, 2020 in Denver CO. The assignment was to discuss applications of Mean Field Games in finance and economics. I need to admit upfront that several of the examples reviewed in this chapter were already discussed in book form. Still, they are here accompanied with discussions of, and references to, works which appeared over the last three years. Moreover, several completely new sections are added to show how recent developments in financial engineering and economics can benefit from being viewed through the lens of the Mean Field Game paradigm. The new financial engineering applications deal with bitcoin mining and the energy markets, while the new economic applications concern models offering a smooth transition between macro-economics and finance, and contract *** Codes 60, 91 © 2020, CC BY.

关键词： Finance