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What affects the performance of POD for the simulation of heat transfer through building component?

Journal of Physics: Conference Series 2021年第1期2069卷

作者： Tianfeng Hou Staf Roels Hans Janssen KU Leuven Department of Civil Engineering Building Physics Section 3001 Leuven Belgium Data Assimilation Research Team RIKEN Center for Computational Science Kobe Japan RIKEN Prediction Science Laboratory Kobe Japan RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program Kobe Japan

The capability of the proper orthogonal decomposition for the simulation of heat transfer in building components is investigated via three applications: linear heat transfer (not coupled to mass transfer), mildly non-linear heat transfer (coupled to air and moisture transfer (hygroscopic)) and highly non-linear heat transfer (coupled to moisture transfer (capillary)). It is shown that increasing non-linearity leads to an increasing number of required construction modes. To further investigate the reason for this degrading performance of POD, the singular values' decay progress from the different training snapshots is addressed in this paper. The results confirm that a fast decay of the singular values implies a high interrelation of the snapshots and a better performance of the POD method.

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Small inter-event times govern epidemic spreading on networks

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Physical Review Research 2020年第2期2卷 023163-023163页

作者： Naoki Masuda Petter Holme Department of Mathematics University at Buffalo State University of New York Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York Buffalo New York 14260-5030 USA Tokyo Tech World Research Hub Initiative (WRHI) Institute of Innovative Research Tokyo Institute of Technology Yokohama 226-8503 Japan

Many aspects of human and animal interaction, such as the frequency of contacts of an individual, the number of interaction partners, and the time between the contacts of two individuals, are characterized by heavy-tailed distributions. These distributions affect the spreading of, e.g., infectious diseases or rumors, often because of impacts of the right tail of the distributions (i.e., the large values). In this paper we show that when it comes to inter-event time distributions, it is not the tail but the small values that control spreading dynamics. We investigate this effect both analytically and numerically for different versions of the susceptible-infected-recovered model on different types of networks.

关键词： Epidemic Epidemic evolution Epidemic growth Epidemic prevalence

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Deep learning of accurate force field of Ferroelectric HfO$_2$

arXiv

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arXiv 2020年

作者： Wu, Jing Zhang, Yuzhi Zhang, Linfeng Liu, Shi Fudan University Shanghai200433 China School of Science Westlake University HangzhouZhejiang310024 China Institute of Natural Sciences Westlake Institute for Advanced Study HangzhouZhejiang310024 China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The discovery of ferroelectricity in HfO2-based thin films opens up new opportunities for using this silicon-compatible ferroelectric to realize low-power logic circuits and high-density non-volatile memories. The functional performances of ferroelectrics are intimately related to their dynamic responses to external stimuli such as electric fields at finite temperatures. Molecular dynamics is an ideal technique for investigating dynamical processes on large length and time scales, though its applications to new materials is often hindered by the limited availability and accuracy of classical force fields. Here we present a deep neural network-based interatomic force field of HfO2 learned from ab initio data using a concurrent learning procedure. The model potential is able to predict structural properties such as elastic constants, equation of states, phonon dispersion relationships, and phase transition barriers of various hafnia polymorphs with accuracy comparable with density functional theory calculations. The validity of this model potential is further confirmed by the reproduction of experimental sequences of temperature-driven ferroelectric-paraelectric phase transitions of HfO2 with isobaric-isothermal ensemble molecular dynamics simulations. We suggest a general approach to extend the model potential of HfO2 to related material systems including dopants and defects. Copyright © 2020, The Authors. All rights reserved.

关键词： Ferroelectricity

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Interference mitigation of adjacent radio frequency signals on a flexible software-defined radio testbed platform 55

Interference mitigation of adjacent radio frequency signals ...

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55th Annual International Telemetering Conference: Cultivating the Next Generation of Range Engineers, ITC 2019

作者： Elahi, Mirza M. Sandoval, Jose C. Gonzalez, Virgilio Corral, Pabel Yasuda, Susumu Gonzalez, Virgilio Computational Science Program University of Texas at El Paso El PasoTX79968 United States Department of Electrical and Computer Engineering University of Texas at El Paso El PasoTX79968 United States U.S. Army Test and Evaluation Command White Sands Missile Range White SandsNM United States

ISBN: (纸本)9781713801887

The radio frequency (RF) spectrum is crowded with users and adjacent frequency users are facing an increase in interference from each other. The spectrum governing body Federal Communications Commission (FCC) has the difficult task of allocating spectral bands for new users for mobile devices using 4G LTE technology. Telemetry (TM) is affected by the adjacent band 4G LTE users in terms of signal degradation. To minimize the interference between adjacent frequency users, several methods can be used. A common but inefficient method separates adjacent band frequencies using guard bands which leaves a big portion of the spectrum unused. Alternatively, adjacent RF signals can be separated using digital filtering techniques with the signal of interest being unharmed and reducing the signal power of the interfering signal. A digital filtering technique includes bandpass filter (BPF) rejection, which has the ability to filter out adjacent interfering signals. This is accomplished by designing bandpass digital filters where the passband and stopband frequencies are adjusted to achieve maximum signal power and reject the interfering signal by reducing its power. A flexible software-defined radio testbed is set up to experiment and analyze this scenario with ease and effective measures. © 2019 International Foundation for Telemetering. All rights reserved.

关键词： Bandpass filters

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Core collapse supernova gravitational wave emission for progenitors of 9.6, 15, and 25M⊙

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Physical Review D 2023年第4期107卷 043008-043008页

作者： Anthony Mezzacappa Pedro Marronetti Ryan E. Landfield Eric J. Lentz R. Daniel Murphy W. Raphael Hix J. Austin Harris Stephen W. Bruenn John M. Blondin O. E. Bronson Messer Jordi Casanova Luke L. Kronzer Department of Physics and Astronomy University of Tennessee 1408 Circle Drive Knoxville Tennessee 37996-1200 USA Physics Division National Science Foundation Alexandria Virginia 22314 USA National Center for Computational Sciences Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge Tennessee 37831-6164 USA Physics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge Tennessee 37831-6354 USA Joint Institute for Nuclear Physics and its Applications Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge Tennessee 37831-6374 USA Department of Physics Florida Atlantic University 777 Glades Road Boca Raton Florida 33431-0991 USA Department of Physics North Carolina State University Raleigh North Carolina 27695-8202 USA Physics Program Community College of Denver P.O. Box 173363 Denver Colorado 80217-3363 USA Department of Aerospace Engineering and Mechanics University of Alabama Box 870280 Tuscaloosa Alabama 35487-0280 USA

We present gravitational wave emission predictions based on three core collapse supernova simulations corresponding to three different progenitor masses. The masses span a large range, between 9.6 and 25M⊙, are all initially nonrotating, and are of two metallicities: zero and solar. We compute both the temporal evolution of the gravitational wave strains for both the plus and the cross polarizations, as well as their spectral decomposition and characteristic strains. The temporal evolution of our zero metallicity 9.6M⊙ progenitor model is distinct from the temporal evolution of our solar metallicity 15M⊙ progenitor model and our zero metallicity 25M⊙ progenitor model. In the former case, the high-frequency gravitational wave emission is largely confined to a brief time period ∼75 ms after bounce, whereas in the latter two cases high-frequency emission does not commence until ∼125 ms after bounce or later. The excitation mechanisms of the high-frequency emission in all three cases correspond to proto-neutron star convection and accretion onto the proto-neutron star from the convective gain layer above it, with the former playing the dominant role for most of the evolution. The low-frequency emission in all three models exhibits very similar behavior. At frequencies below ∼250 Hz, gravitational waves are emitted by neutrino-driven convection and the standing accretion shock instability (SASI). This emission extends throughout the simulations when a gain region is present. In all three models, explosion is observed at ∼125, ∼500, and ∼250 ms after bounce in the 9.6, 15, and 25M⊙ progenitor models, respectively. At these times, the low-frequency gravitational wave emission is joined by very low-frequency emission, below ∼10 Hz. These very low-frequency episodes are the result of explosion and begin at the above designated explosion times in each of our models. Our characteristic strains tell us that, in principle, all three gravitational wave signals would be detec

关键词： Gravitation Gravitational waves Novae & supernovae Transient & explosive astronomical phenomena

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A linked data graph approach to integration of immunological data

A linked data graph approach to integration of immunological...

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IEEE International Conference on Bioinformatics and Biomedicine

作者： Syed Ahmad Chan Bukhari Jeff Mandell Steven H. Kleinstein Kei-Hoi Cheung Division of Computer Science Mathematics and Science Lesley H. & William L. Collins College of Professional Studies St. John's University Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Pathology Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Emergency Medicine and Yale Center for Medical Informatics Computationa Biology and Bioinformaticcs Yale University

ISBN: (纸本)9781728118680

Systems biology involves the integration of multiple data types (across different data sources) to offer a more complete picture of the biological system being studied. While many existing biological databases are implemented using the traditional SQL (Structured Query Language) database technology, NoSQL database technologies have been explored as a more relationship-based, flexible and scalable method of data integration. In this paper, we describe how to use the Neo4J graph database to integrate a variety of types of data sets in the context of systems vaccinology. Specifically, we have converted into a common graph model diverse types of vaccine response measurement data from the NIH/NIAID ImmPort data repository, pathway data from Reactome, influenza virus strains from WHO, and taxonomic data from NCBI Taxon. While Neo4J provides a graph-based query language (Cypher) for data retrieval, we develop a web-based dashboard for users to easily browse and visualize data without the need to learn Cypher. In addition, we have prototyped a natural language query interface for users to interact with our system. In conclusion, we demonstrate the feasibility of using a graph-based database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to reveal novel relationships among heterogeneous biological data.

关键词： ontology knowledgebase graph database immunology influenza vaccine graphic library Knowledge Bases Influenza Vaccines Ontology Immunology data integration Passwords DNA Integration integration data types Data sources SQL

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Total Marrow and Lymphoid Irradiation (TMLI) at a Dose of 2000cGy in Combination with Post-Transplant Cyclophosphamide (PTCy)-Based Graft Versus Host Disease (GvHD) Prophylaxis Is Safe and Associated with Favorable GvHD-Free/Relapse-Free Survival at 1 Year in Patients with Acute Myeloid Leukemia (AML)

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BLOOD 2020年 136卷 41-42页

作者： Stein, Anthony S. Al Malki, Monzr M. Yang, Dongyun Palmer, Joycelynne Tsai, Ni-Chun Aldoss, Ibrahim Ali, Haris Aribi, Ahmed Artz, Andrew S. Farol, Len Hui, Susanta Karanes, Chatchada Khaled, Samer Liu, An Marcucci, Guido Nakamura, Ryotaro Pullarkat, Vinod A. Radany, Eric Rosenthal, Joseph Salhotra, Amandeep Sanchez, James F. Spielberger, Ricardo Snyder, David S. Forman, Stephen J. Wong, Jeffrey Gehr Family Center for Leukemia Research City of Hope Duarte CA Department of Computational and Quantitative Medicine-BRI City of Hope National Medical Center Duarte CA Bone Marrow Transplant Program Southern California Kaiser Permanente Los Angeles CA Department of Radiation Oncology Beckman Research Institute City of Hope Duarte CA Department of Hematology and Hematopoietic Cell Transplantation City of Hope Duarte CA Department of Radiation Oncology City of Hope Duarte CA Department of Hematologic Malignancies Translational Science Gehr Family Center for Leukemia Research Hematologic Malignancies and Stem Cell Transplantation Institute Beckman Research Institute City of Hope Monrovia CA Department of Pediatrics City of Hope Duarte CA

Background : Allogeneic hematopoietic cell transplantation (alloHCT) is the approach that offers the highest curative rate for acute myelogenous leukemia (AML) with intermediate or high-risk cytogenetics. Graft versus host disease (GvHD) has remained the main cause of post-transplantation mortality and morbidity, despite advances in prophylaxis and therapy, adding significant economic burden and affecting quality of life. It would be desirable to reduce the rate of GvHD among patients in complete remission (CR) without increasing the risk of relapse. In this study, we have developed a novel conditioning regimen of total marrow and lymphoid irradiation (TMLI) at 2000 cGy, together with post-transplant cyclophosphamide (PTCy), to 1) reduce the possibly increased risk of relapse from PTCy, by using escalated radiation doses of TMLI, as increasing radiation doses has the potential to decrease the post-transplantation relapse rate (Blood, vol 76, pp. 1867-1871, 1990); and 2) reduce the risk of chronic GvHD by using PTCy. The major goal of this pilot study of TMLI and PTCy (***: NCT03467386), was to thus improve GvHD-free/relapse-free survival (GRFS), reported to be 45% from total body irradiation (TBI) and tacrolimus/sirolimus prophylaxis (BBMT, vol 26(2), pp. 292-299, 2020), in patients with AML in remission. Patients and Methods : A total of 18 patients were enrolled and treated (see Table) between March 2018 and December 2019. Key criteria were ages 18 to 60, first or second CR, minimal residual disease negative by multi-color flow cytometry, and normal organ function. TMLI was administered on days -4 to 0 without addition of chemotherapy. The radiation dose for all patients (n=18) was 2000 cGy, delivered in 200 cGy fractions twice daily. The radiation dose delivered to the liver and brain was kept at 1200 cGy. Remaining organs were considered non-targeted. All patients received peripheral blood stem cells on day 0. Cyclophosphamide was given on days +3

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Rapid identification and monitoring of cooking oil fume-based toxic volatile organic aldehydes in lung tissue for predicting exposure level and cancer risks

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Chemosphere 2023年第1期339卷 139704页

作者： Prakasham, Karthikeyan Gurrani, Swapnil Wu, Chia-Fang Wu, Ming-Tsang Hsieh, Tusty-Jiuan Peng, Chiung-Yu Huang, Po-Chin Krishnan, Anbarasu Tsai, Pei-Chien Lin, Yu-Chia Tsai, Bongee Lin, Yuan-Chung Ponnusamy, Vinoth Kumar Kaohsiung City807 Taiwan Kaohsiung City807 Taiwan International Master Program of Translational Medicine College of Engineering and Science National United University Miaoli Taiwan Kaohsiung City807 Taiwan Department of Public Health College of Health Sciences Kaohsiung Medical University Kaohsiung City807 Taiwan Miaoli County 35053 Taiwan Department of Computational Biology Institute of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Tamil Nadu Chennai602105 India Kaohsiung City807 Taiwan Corporation No.392 Yucheng Rd. Zuoying District. Kaohsiung City813 Taiwan Center for Emerging Contaminants Research National Sun Yat-Sen University Kaohsiung City804 Taiwan Institute of Environmental Engineering National Sun Yat-Sen University Kaohsiung City804 Taiwan Kaohsiung Medical University Kaohsiung City807 Taiwan Department of Medical Research China Medical University Hospital China Medical University Taichung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan

Cooking oil fumes (COFs) comprised of a mixture of cancer-causing volatile organic aldehydes (VOAs), particularly trans, trans-2,4-decadienal (t,t-DDE), 4-hydroxy-hexenal (4-HHE), and 4-hydroxy-nonenal (4-HNE). Monitoring toxic VOAs levels in people exposed to different cooking conditions is vital to predicting the cancer risk. For this purpose, we developed a fast tissue extraction (FaTEx) technique combined with UHPLC-MS/MS to monitor three toxic VOAs in mice lung tissue samples. FaTEx pre-treatment protocol was developed by combining two syringes for extraction and clean-up process. The various procedural steps affecting the FaTEx sample pre-treatment process were optimized to enhance the target VOAs’ extraction efficiency from the sample matrix. Under the optimal experimental conditions, results exhibit good correlation coefficient values > 0.99, detection limits were between 0.5–3 ng/g, quantification limits were between 1–10 ng/g, and the matrix effect was © 2023 Elsevier Ltd

关键词： Diseases

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Review: Precision medicine and driver mutations: computational methods, functional assays and conformational principles for interpreting cancer drivers (vol 15, e1006658, 2019)

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PLOS computational BIOLOGY 2019年第6期15卷 e1006658-e1006658页

作者： Nussinov, Ruth Jang, Hyunbum Tsai, Chung-Jung Cheng, Feixiong Computational Structural Biology Section Basic Science Program Frederick National Laboratory for Cancer Research National Cancer Institute Frederick Maryland United States of America Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine Tel Aviv University Tel Aviv Israel Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland Ohio United States of America Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine Case Western Reserve University Cleveland Ohio United States of America

At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.

关键词： INDIVIDUALIZED medicine CANCER genetics MUTATION (Biology) ONCOLOGY CANCER treatment EXOMES PHARMACOLOGY TUMOR genetics

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Hyper-molecules: On the representation and recovery of dynamical structures, with application to flexible macro-molecular structures in cryo-EM

arXiv

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arXiv 2019年

作者： Lederman, Roy R. Andén, Joakim Singer, Amit Department of Statistics and Data Science Yale University New HavenCT United States Center for Computational Mathematics Flatiron Institute New YorkNY United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States

Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose orientations and positions are unknown. The molecular structures are not rigid objects, but flexible objects involved in dynamical processes. The different conformations are exhibited by different instances of the macromolecule observed in a cryo-EM experiment, each of which is recorded as a particle image. The range of conformations and the conformation of each particle are not known a priori;one of the great promises of cryo-EM is to map this conformation space. Remarkable progress has been made in determining rigid structures from homogeneous samples of molecules in spite of the unknown orientation of each particle image and significant progress has been made in recovering a few distinct states from mixtures of rather distinct conformations, but more complex heterogeneous samples remain a major challenge. We introduce the "hyper-molecule" framework for modeling structures across different states of heterogeneous molecules, including continuums of states. The key idea behind this framework is representing heterogeneous macromolecules as high-dimensional objects, with the additional dimensions representing the conformation space. This idea is then refined to model properties such as localized heterogeneity. In addition, we introduce an algorithmic framework for recovering such maps of heterogeneous objects from experimental data using a Bayesian formulation of the problem and Markov chain Monte Carlo (MCMC) algorithms to address the computational challenges in recovering these high dimensional hyper-molecules. We demonstrate these ideas in a prototype applied to synthetic data. Copyright © 2019, The Authors. All rights reserved.

关键词： Medical imaging

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