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Towards Implementation of the Pressure-Regulated, Feedback-Modulated Model of Star Formation in Cosmological Simulations: Methods and Application to TNG

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arXiv 2024年

作者： Hassan, Sultan Ostriker, Eve C. Kim, Chang-Goo Bryan, Greg L. Burger, Jan D. Fielding, Drummond B. Forbes, John C. Genel, Shy Hernquist, Lars Jeffreson, Sarah M.R. Motwani, Bhawna Smith, Matthew C. Somerville, Rachel S. Steinwandel, Ulrich P. Teyssier, Romain Center for Cosmology and Particle Physics Department of Physics New York University 726 Broadway New YorkNY10003 United States Center for Computational Astrophysics Flatiron Institute 162 5th Ave New YorkNY10010 United States Department of Physics & Astronomy University of the Western Cape Cape Town7535 South Africa Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Institute for Advanced Study 1 Einstein Drive PrincetonNJ08540 United States Department of Astronomy Columbia University 550 W 120th Street New YorkNY10027 United States Max-Planck-Institut für Astrophysik Karl-Schwarzschild-Str. 1 GarchingD-85748 Germany Department of Astronomy Cornell University IthacaNY14853 United States School of Physical and Chemical Sciences-Te Kura Matū University of Canterbury Private Bag 4800 Christchurch8140 New Zealand Columbia Astrophysics Laboratory Columbia University 550 West 120th Street New YorkNY10027 United States Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA United States Program in Applied and Computational Mathematics Princeton University Fine Hall Washington Road PrincetonNJ08544-1000 United States

Traditional star formation subgrid models implemented in cosmological galaxy formation simulations, such as that of Springel & Hernquist (2003, hereafter SH03), employ adjustable parameters to satisfy constraints measured in the local Universe. In recent years, however, theory and spatially-resolved simulations of the turbulent, multiphase, star-forming ISM have begun to produce new first-principles models, which when fully developed can replace traditional subgrid prescriptions. This approach has advantages of being physically motivated and predictive rather than empirically tuned, and allowing for varying environmental conditions rather than being tied to local Universe conditions. As a prototype of this new approach, by combining calibrations from the TIGRESS numerical framework with the Pressure-Regulated Feedback-Modulated (PRFM) theory, simple formulae can be obtained for both the gas depletion time and an effective equation of state. Considering galaxies in TNG50, we compare the "native" simulation outputs with post-processed predictions from PRFM. At TNG50 resolution, the total midplane pressure is nearly equal to the total ISM weight, indicating that galaxies in TNG50 are close to satisfying vertical equilibrium. The measured gas scale height is also close to theoretical equilibrium predictions. The slopes of the effective equations of states are similar, but with effective velocity dispersion normalization from SH03 slightly larger than that from current TIGRESS simulations. Because of this and the decrease in PRFM feedback yield at high pressure, the PRFM model predicts shorter gas depletion times than the SH03 model at high densities and redshift. Our results represent a first step towards implementing new, numerically calibrated subgrid algorithms in cosmological galaxy formation simulations. Copyright © 2024, The Authors. All rights reserved.

关键词： Cosmology

Numerical meshless solution of high-dimensional sine-gordon equations via fourier HDMR-HC approximation

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arXiv 2019年

作者： Xu, Xin Luo, Xiaopeng Rabitz, Herschel Department of Chemistry Princeton University PrincetonNJ08544 United States School of Managment and Engineering Nanjing University Nanjing210008 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

In this paper, an implicit time stepping meshless scheme is proposed to find the numerical solution of high-dimensional sine-Gordon equations (SGEs) by combining the high dimensional model representation (HDMR) and the Fourier hyperbolic cross (HC) approximation. To ensure the sparseness of the relevant coefficient matrices of the implicit time stepping scheme, the whole domain is first divided into a set of subdomains, and the relevant derivatives in high-dimension can be separately approximated by the Fourier HDMR-HC approximation in each subdomain. The proposed method allows for stable large time-steps and a relatively small number of nodes with satisfactory accuracy. The numerical examples show that the proposed method is very attractive for simulating the high-dimensional SGEs. Copyright © 2019, The Authors. All rights reserved.

关键词： Numerical methods

Structural basis and synergism of ATP and Na⁺ activation in bacterial K⁺ uptake system KtrAB

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Nature Communications 2024年第1期15卷 3850页

作者： Chiang, Wesley Tien Chang, Yao-Kai Hui, Wei-Han Chang, Shu-Wei Liao, Chen-Yi Chang, Yi-Chuan Chen, Chun-Jung Wang, Wei-Chen Lai, Chien-Chen Wang, Chun-Hsiung Luo, Siou-Ying Huang, Ya-Ping Chou, Shan-Ho Horng, Tzyy-Leng Hou, Ming-Hon Muench, Stephen P. Chen, Ren-Shiang Tsai, Ming-Daw Hu, Nien-Jen Graduate Institute of Biochemistry National Chung Hsing University Taichung 402202 Taiwan Institute of Biological Chemistry Academia Sinica Taipei 115201 Taiwan Department of Civil Engineering National Taiwan University Taipei 106319 Taiwan Department of Biomedical Engineering National Taiwan University Taipei 10663 Taiwan Life Science Group Scientific Research Division National Synchrotron Radiation Research Center Hsinchu 30092 Taiwan Institute of Molecular Biology National Chung Hsing University Taichung 402202 Taiwan Graduate Institute of Chinese Medical Science China Medical University Taichung 406040 Taiwan Department of Applied Mathematics Feng Chia University Taichung 407102 Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung 402202 Taiwan School of Biomedical Sciences Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT United Kingdom Department of Life Science Tunghai University Taichung 407224 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 106319 Taiwan Ph.D Program in Translational Medicine National Chung Hsing University Taichung 402202 Taiwan

The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated...

The K⁺ uptake system KtrAB is essential for bacterial survival in low K⁺ environments. The activity of KtrAB is regulated by nucleotides and Na⁺. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na⁺ activates KtrAB and the Na⁺ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na⁺, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na⁺ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K⁺ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na⁺ in activating BsKtrAB is likely applicable to Na⁺-activated K⁺ channels in central nervous system. © The Author(s) 2024.

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Featurized bidirectional GAN: Adversarial defense via adversarially learned semantic inference

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arXiv 2018年

作者： Bao, Ruying Liang, Sihang Wang, Qingcan Program in Applied and Computational Mathematics Princeton University Department of Physics Princeton University

Deep neural networks have been demonstrated to be vulnerable to adversarial attacks, where small perturbations intentionally added to the original inputs can fool the classifier. In this paper, we propose a defense method, Featurized Bidirectional Generative Adversarial Networks (FBGAN), to extract the semantic features of the input and filter the non-semantic perturbation. FBGAN is pre-trained on the clean dataset in an unsupervised manner, adversarially learning a bidirectional mapping between the high-dimensional data space and the low-dimensional semantic space;also mutual information is applied to disentangle the semantically meaningful features. After the bidirectional mapping, the adversarial data can be reconstructed to denoised data, which could be fed into any pre-trained classifier. We empirically show the quality of reconstruction images and the effectiveness of defense. Copyright © 2018, The Authors. All rights reserved.

关键词： Generative adversarial networks

Meshless Hermite-HDMR finite difference method for high-dimensional Dirichlet problems

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arXiv 2019年

作者： Luo, Xiaopeng Xu, Xin Rabitz, Herschel Department of Chemistry Princeton University PrincetonNJ08544 United States School of Managment and Engineering Nanjing University Nanjing210008 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

In this paper, a meshless Hermite-HDMR finite difference method is proposed to solve high-dimensional Dirichlet problems. The approach is based on the local Hermite-HDMR expansion with an additional smoothing technique. First, we introduce the HDMR decomposition combined with the multiple Hermite series to construct a class of Hermite-HDMR approximations, and the relevant error estimate is theoretically built in a class of Hermite spaces. It can not only provide high order convergence but also retain good scaling with increasing dimensions. Then the Hermite-HDMR based finite difference method is particularly proposed for solving high-dimensional Dirichlet problems. By applying a smoothing process to the Hermite-HDMR approximations, numerical stability can be guaranteed even with a small number of nodes. Numerical experiments in dimensions up to 30 show that resulting approximations are of very high quality. Copyright © 2019, The Authors. All rights reserved.

关键词： Finite difference method

Contribution of information technology (IT) system in overcoming neonatal jaundice: a systematic literature review

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Journal of Physics: Conference Series 2020年第1期1524卷

作者： D Anggraini M N Widyawati S Suryono Master of Applied Science in Midwifery Poltekkes Kemenkes Semarang Indonesia Postgraduate Applied Science Midwifery Program Poltekkes Kemenkes Semarang Indonesia Departement of Physics Faculty of Science and Mathematics Universitas Diponegoro Semarang Indonesia

Information technology systems can improve efficiency, quality of service, security and improve the quality of diagnosis, especially in the incidence of neonatal jaundice, because the incidence of jaundice that is not monitored can cause increasingly severe problems so that it can cause kernicterus and can also cause death in neonatal. This paper is focused on analyzing the contribution of information technology systems to health problems especially neonatal jaundice. The study design uses a systematic literature review with international journals in electronic databases. Journal criteria used the Randomized Controlled Trial (RCT) technique from 2011-2019. This systematic literature review concludes that information technology systems have a role in health care, wherefrom several technologies have proven to be able to detect, diagnose, treatment and education that is easy, fast, effective and can be used whenever needed in overcoming the problem of neonatal jaundice. However, the use of information technology systems has not been comprehensive so that it needs development especially in areas with limited access.

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An algorithm based on Voronoi diagrams for the multi-stream multi-source multicast routing problem

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International Journal of Innovative Computing and Applications 2018年第4期9卷 216-229页

作者： De Andrade, Romerito Campos Goldbarg, Marco César Goldbarg, Elizabeth Ferreira Gouveâ Postgraduate Program in Systems and Computation Federal University of Rio Grande Do Norte Campus Universitário Lagoa Nova Natal RN Brazil Department of Informatics and Applied Mathematics Federal University of Rio Grande Do Norte Campus Universitário Lagoa Nova Natal RN Brazil

In this study, we present a new heuristic for the multi-stream multi-source multicast routing problem. The core of the heuristic proposed in this study is based on a generalisation of Voronoi diagrams in graphs. It allows building the trees needed to serve the demands of multiple sessions efficiently. Also, the proposed algorithm supports multiple sources. We performed an extensive experimental analysis of different network and problem configurations such as the number of sessions, nodes, sources and participants per session. We compare the proposed algorithm to heuristics proposed previously. The results of the experiments showed that the heuristic proposed in this study finds high-quality solutions efficiently. © 2018 Inderscience Enterprises Ltd.

关键词： Multicasting

Quality of internal representation shapes learning performance in feedback neural networks

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arXiv 2020年

作者： Susman, Lee Mastrogiuseppe, Francesca Brenner, Naama Barak, Omri Interdisciplinary Program in Applied Mathematics Technion Israel Institute of Technology Haifa32000 Israel Network Biology Research Laboratories Technion Israel Institute of Technology Haifa32000 Israel Gatsby Computational Neuroscience Unit University College London London United Kingdom Dept. of Chemical Engineering Technion Israel Institute of Technology Haifa32000 Israel Rappaport Faculty of Medicine Technion Israel Institute of Technology Haifa32000 Israel

A fundamental feature of complex biological systems is the ability to form feedback interactions with their environment. A prominent model for studying such interactions is reservoir computing, where learning acts on low-dimensional bottlenecks. Despite the simplicity of this learning scheme, the factors contributing to or hindering the success of training in reservoir networks are in general not well understood. In this work, we study non-linear feedback networks trained to generate a sinusoidal signal, and analyze how learning performance is shaped by the interplay between internal network dynamics and target properties. By performing exact mathematical analysis of linearized networks, we predict that learning performance is maximized when the target is characterized by an optimal, intermediate frequency which monotonically decreases with the strength of the internal reservoir connectivity. At the optimal frequency, the reservoir representation of the target signal is high-dimensional, de-synchronized, and thus maximally robust to noise. We show that our predictions successfully capture the qualitative behaviour of performance in non-linear networks. Moreover, we find that the relationship between internal representations and performance can be further exploited in trained non-linear networks to explain behaviours which do not have a linear counterpart. Our results indicate that a major determinant of learning success is the quality of the internal representation of the target, which in turn is shaped by an interplay between parameters controlling the internal network and those defining the task. © 2020, CC BY.

关键词： Quality control

Noise induces continuous and noncontinuous transitions in neuronal interspike intervals range

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arXiv 2020年

作者： Protachevicz, P.R. Santos, M.S. Seifert, E.G. Gabrick, E.C. Borges, F.S. Borges, R.R. Trobia, J. Szezech, J.D. Iarosz, K.C. Caldas, I.L. Antonopoulos, C.G. Xu, Y. Viana, R.L. Batista, A.M. Graduate Program in Science-Physics State University of Ponta Grossa Ponta Grossa84030-900 Institute of Physics University of Saõ Paulo Saõ Paulo05508-900 Brazil Department of Physics State University of Ponta Grossa Ponta Grossa84030-900 Center ForMathematics Computation and Cognition Federal University of ABC Sao Bernardo do Campo09606-045 Department of Mathematics Federal University of Technology Paraná Ponta Grossa84016-210 Department of Mathematics and Statistics State University of Ponta Grossa Ponta Grossa84030-900 Faculdade de Telêmaco Borba FATEB Telemaco Borba84266-010 Brazil Department of Mathematical Sciences University of Essex Wivenhoe ParkCO43SQ United Kingdom Department of Applied Mathematics Northwestern Polytechnical University Xi'an710072 Department of Physics Federal University of Paraná Curitiba82590-300 Brazil

Noise appears in the brain due to various sources, such as ionic channel fluctuations and synaptic events. They affect the activities of the brain and influence neuron action potentials. Stochastic differential equations have been used to model firing patterns of neurons subject to noise. In this work, we consider perturbing noise in the adaptive exponential integrate-and-fire (AEIF) neuron. The AEIF is a two-dimensional model that describes different neuronal firing patterns by varying its parameters. Noise is added in the equation related to the membrane potential. We show that a noise current can induce continuous and noncontinuous transitions in neuronal interspike intervals. Moreover, we show that the noncontinuous transition occurs mainly for parameters close to the border between tonic spiking and burst activities of the neuron without noise. Copyright © 2020, The Authors. All rights reserved.

关键词： Neurons