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Special issue on genome wide association study

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Quantitative Biology 2021年第2期9卷 105-106页

作者： Lin Hou Qiongshi Lu Can Yang Hongyu Zhao Center for Statistical Science Department of Industrial EngineeringMOE Key Laboratory of BioinformaticsSchool of Life SciencesTsinghua UniversityBeijing 100084China Department of Biostatistics and Medical Informatics Department of StatisticsCenter for Demography of Health and AgingUniversity of Wisconsin-MadisonWl 53726USA Department of Mathematics the Hong Kong University of Science and TechnologyHong KongChina Department of Biostatistics Yale School of Public HealthNew HavenCT 06510USA Department of Genetics Yale UniversityNew HavenCT 06510USA Program of Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06510USA

Since the first success of genome wide association study(GWAS)was reported in 2005 by Hoh and colleagues on the identification of a major gene for age related macular degeneration,many thousands of published studies have reported reproducible association signals between hundreds of thousands of genetic variants and thousands of traits and diseases in the past 16 *** is a growing number of biobanks with up to one million participants developed across the world to facilitate genetic studies of complex traits through ***,many consortium projects have been initiated to collect diverse types of data that have proved very valuable for integrated analysis of GWAS *** rich data present both great opportunities and challenges to scientists on data management,computation,analysis,integration,and *** special issue of Quantitative Biology collects nine papers that cover major progresses,challenges,and future directions for GWAS analysis.

关键词： hundreds GWAS initiated

Breaking Mechanical Holography in Combinatorial Metamaterials

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arXiv 2024年

作者： Sirote-Katz, Chaviva Palti, Ofri Spiro, Naomi Kálmán, Tamás Shokef, Yair Department of Biomedical Engineering Tel Aviv University Tel Aviv69978 Israel The Future Scientists Center Alpha Program Tel Aviv Youth University Tel Aviv69978 Israel University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mathematics Institute of Science Tokyo H-214 2-12-1 Ookayama Tokyo Meguro-ku152-8551 Japan Hiroshima University Higashi-Hiroshima Hiroshima739-8526 Japan School of Mechanical Engineering Tel Aviv University Tel Aviv69978 Israel Center for Computational Molecular and Materials Science Tel Aviv University Tel Aviv69978 Israel Center for Physics and Chemistry of Living Systems Tel Aviv University Tel Aviv69978 Israel

Combinatorial mechanical metamaterials are made of anisotropic, flexible blocks, such that multiple metamaterials may be constructed using a single block type, and the system’s response strongly depends on the mutual orientations of the blocks within the lattice. We study a family of possible block types for the square, honeycomb, and cubic lattices. Blocks that are centrally symmetric induce holographic order, such that mechanical compatibility (meaning that blocks do not impede each other’s motion) implies bulk-boundary coupling. With them, one can design a compatible metamaterial that will deform in any desired texture only on part of its boundary. With blocks that break holographic order, we demonstrate how to design the deformation texture on the entire boundary. Correspondingly, the number of compatible holographic metamaterials scales exponentially with the boundary, while in non-holographic cases we show that it scales exponentially with the bulk. © 2024, CC BY.

关键词： Holography

Sensitivity Analysis of Wind Energy Resources with Bayesian non-Gaussian and nonstationary Functional ANOVA

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arXiv 2021年

作者： Zhang, Jiachen Crippa, Paola Genton, Marc G. Castruccio, Stefano Department of Applied and Computational Mathematics and Statistics University of Notre Dame United States Department of Civid and Environmental Engineering and Geoscience University of Notre Dame United States Statistics Program King Abdullah University of Science and Technology Saudi Arabia

The transition from non-renewable to renewable energies represents a global societal challenge, and developing a sustainable energy portfolio is an especially daunting task for developing countries where little to no information is available regarding the abundance of renewable resources such as wind. Weather model simulations are key to obtain such information when observational data are scarce and sparse over a country as large and geographically diverse as Saudi Arabia. However, output from such models is uncertain, as it depends on inputs such as the parametrization of the physical processes and the spatial resolution of the simulated domain. In such situations, a sensitivity analysis must be performed and the input may have a spatially heterogeneous influence of wind. In this work, we propose a latent Gaussian functional analysis of variance (ANOVA) model that relies on a nonstationary Gaussian Markov random field approximation of a continuous latent process. The proposed approach is able to capture the local sensitivity of Gaussian and non-Gaussian wind characteristics such as speed and threshold exceedances over a large simulation domain, and a continuous underlying process also allows us to assess the effect of different spatial resolutions. Our results indicate that (1) the non-local planetary boundary layer scheme and high spatial resolution are both instrumental in capturing wind speed and energy (especially over complex mountainous terrain), and (2) the impact of planetary boundary layer scheme and resolution on Saudi Arabia’s planned wind farms is small (at most 1.4%). Thus, our results lend support for the construction of these wind farms in the next decade. © 2021, CC BY-NC-ND.

关键词： Sensitivity analysis

Anomalous suppression of large-scale density fluctuations in classical and quantum spin liquids

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arXiv 2025年

作者： Chen, Duyu Samajdar, Rhine Jiao, Yang Torquato, Salvatore Materials Research Laboratory University of California Santa BarbaraCA93106 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Center for Theoretical Science Princeton University PrincetonNJ08544 United States Materials Science and Engineering Arizona State University TempeAZ85287 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Materials Institute Princeton University PrincetonNJ08540 United States Program in Applied and Computational Mathematics PrincetonNJ08544 United States

Classical spin liquids (CSLs) are intriguing states of matter that do not exhibit long-range magnetic order and are characterized by an extensive ground-state degeneracy. Adding quantum fluctuations, which induce dynamics between these different classical ground states, can give rise to quantum spin liquids (QSLs). QSLs are highly entangled quantum phases of matter characterized by fascinating emergent properties, such as fractionalized excitations and topological order. One such exotic quantum liquid is the Z2 QSL, which can be regarded as a resonating valence bond (RVB) state formed from superpositions of dimer coverings of an underlying lattice. In this work, we unveil a hidden large-scale structural property of archetypal CSLs and QSLs known as hyperuniformity, i.e., normalized infinite-wavelength density fluctuations are completely suppressed in these systems. In particular, we first demonstrate that classical ensembles of close-packed dimers and their corresponding quantum RVB states are perfectly hyperuniform in general. Subsequently, we focus on a ruby-lattice spin liquid that was recently realized in a Rydberg-atom quantum simulator, and show that the QSL remains effectively hyperuniform even in the presence of a finite density of spinon and vison excitations, as long as the dimer constraint is still largely preserved. Moreover, we demonstrate that metrics based on the framework of hyperuniformity can be used to distinguish the QSL from other proximate quantum phases. These metrics can help identify potential QSL candidates, which can then be further analyzed using more advanced, computationally-intensive quantum numerics to confirm their status as true QSLs. © 2025, CC BY-NC-ND.

关键词： Quantum entanglement

Finite-size effects on the convergence time in continuous-opinion dynamics

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Physical Review E 2021年第1期104卷 014309-014309页

作者： Hang-Hyun Jo Naoki Masuda Department of Physics The Catholic University of Korea Bucheon 14662 Republic of Korea Department of Mathematics State University of New York at Buffalo Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo New York 14260-5030 USA

We study finite-size effects on the convergence time in a continuous-opinion dynamics model. In the model, each individual's opinion is represented by a real number on a finite interval, e.g., [0,1], and a uniformly randomly chosen individual updates its opinion by partially mimicking the opinion of a uniformly randomly chosen neighbor. We numerically find that the characteristic time to the convergence increases as the system size increases according to a particular functional form in the case of lattice networks. In contrast, unless the individuals perfectly copy the opinion of their neighbors in each opinion updating, the convergence time is approximately independent of the system size in the case of regular random graphs, uncorrelated scale-free networks, and complete graphs. We also provide a mean-field analysis of the model to understand the case of the complete graph.

关键词： Complex systems Nonequilibrium statistical mechanics Social systems Homogeneous networks Scale free & inhomogeneous networks Social dynamics Master equation Monte Carlo methods Network Models

A deep potential model with long-range electrostatic interactions

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arXiv 2021年

作者： Zhang, Linfeng Wang, Han Muniz, Maria Carolina Panagiotopoulos, Athanassios Z. Car, Roberto Weinan, E. DP Technology Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Department of Chemical and Biological Engineering Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Program in Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States School of Mathematical Sciences Peking University Beijing100871 China AI for Science Institute Beijing China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make possible molecular simulations with the accuracy of quantum mechanical density functional theory, at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei+core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the deep potential long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples, the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal. © 2021, CC BY.

关键词： Electrostatics

computational models of astrocyte function at glutamatergic synapses

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arXiv 2024年

作者： Lenk, Kerstin Denizot, Audrey Genocchi, Barbara Seppälä, Ippa Taheri, Marsa Nadkarni, Suhita Institute of Neural Engineering Graz University of Technology Graz Austria BioTechMed Graz8010 Austria Theoretical Sciences Visiting Program Okinawa Institute of Science and Technology Graduate University Onna Japan Okinawa Institute of Science and Technology Computational Neuroscience Unit Onna-Son Japan AIstroSight Inria Hospices Civils de Lyon Université Claude Bernard Lyon 1 Villeurbanne France University of Lyon LIRIS UMR5205 Villeurbanne France Faculty of Medicine and Health Technology Tampere University Tampere Finland Department of Psychology and Speech-Language Pathology University of Turku Turku Finland Department of Neurobiology University of California Los AngelesCA United States Department of Biology Indian Institute of Science Education and Research Pune India

At tripartite synapses, astrocytes are in close contact with neurons and contribute to various functions, from synaptic transmission, maintenance of ion homeostasis and glutamate uptake to metabolism. However, disentangling the precise contribution of astrocytes to those phenomena and the underlying biochemical mechanisms is remarkably challenging. This notably results from their highly ramified morphology, the nanoscopic size of the majority of astrocyte processes, and the poorly understood information encoded by their spatiotemporally diverse calcium signals. This book chapter presents selected computational models of the involvement of astrocytes in glutamatergic transmission. The goal of this chapter is to present representative models of astrocyte function in conjunction with the biological questions they can investigate. © 2024, CC BY-NC-SA.

关键词： Calcium

Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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The effects of surface fossil magnetic fields on massive star evolution: V. Models at low metallicity

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arXiv 2024年

作者： Keszthelyi, Z. Puls, J. Chiaki, G. Nagakura, H. Ud-Doula, A. Takiwaki, T. Tominaga, N. Center for Computational Astrophysics Division of Science National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan LMU München Universitätssternwarte Scheinerstr. 1 München81679 Germany National Institute of Technology Kochi College 200-1 Monobe Kochi Nankoku783-8508 Japan Penn State Scranton 120 Ridge View Drive DunmorePA18512 United States Astronomical Science Program Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Department of Physics Faculty of Science and Engineering Konan University 8-9-1 Okamoto Hyogo Kobe658-8501 Japan

At metallicities lower than that of the Small Magellanic Cloud, it remains essentially unexplored how fossil magnetic fields, forming large-scale magnetospheres, could affect the evolution of massive stars, thereby impacting the fundamental building blocks of the early Universe. We extend our stellar evolution model grid with representative calculations of main-sequence, single-star models with initial masses of 20 and 60 M☉, including appropriate changes for low-metallicity environments (Z = 10−3–10−6). We scrutinise the magnetic, rotational, and chemical properties of the models. When lowering the metallicity, the rotational velocities can become higher and the tendency towards quasi-chemically homogeneous evolution increases. While magnetic fields aim to prevent the development of this evolutionary channel, the weakening stellar winds lead to less efficient magnetic braking in our models. Since the stellar radius is almost constant during a blueward evolution caused by efficient chemical mixing, the surface magnetic field strength remains unchanged in some models. We find core masses at the terminal-age main sequence between 22 and 52 M☉ for initially 60 M☉ models. This large difference is due to the vastly different chemical and rotational evolution. We conclude that in order to explain chemical species and, in particular, high nitrogen abundances in the early Universe, the adopted stellar models need to be under scrutiny. The assumptions regarding wind physics, chemical mixing, and magnetic fields will strongly impact the model predictions. © 2024, CC BY.

关键词： Giant stars