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arXiv 2017年

作者： Al-Radhawi, M. Ali Vecchio, Domitilla Del Sontag, Eduardo D. Department of Mechanical Engineering Massachusetts Institute of Technology CambridgeMA02139-4307 United States Departments of Bioengineering and of Electrical and Computer Engineering Northeastern University BostonMA02115 United States Harvard Program in Therapeutic Science Harvard Medical School BostonMA02115 United States

Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states of complex nonlinear systems: stable attractors in deterministic models or modes of stationary distributions in stochastic descriptions. We provide theoretical and practical characterizations of these landscapes, specifically focusing on stochastic slow promoter kinetics, a time scale relevant when transcription factor binding and unbinding are affected by epigenetic processes like DNA methylation and chromatin remodeling. In this case, largely unexplored except for numerical simulations, adiabatic approximations of promoter kinetics are not appropriate. In contrast to the existing literature, we provide rigorous analytic characterizations of multiple modes. A general formal approach gives insight into the influence of parameters and the prediction of how changes in GRN wiring, for example through mutations or artificial interventions, impact the possible number, location, and likelihood of alternative states. We adapt tools from the mathematical field of singular perturbation theory to represent stationary distributions of Chemical Master Equations for GRNs as mixtures of Poisson distributions and obtain explicit formulas for the locations and probabilities of metastable states as a function of the parameters describing the system. As illustrations, the theory is used to tease out the role of cooperative binding in stochastic models in comparison to deterministic models, and applications are given to various model systems, such as toggle switches in isolation or in communicating populations, a synthetic oscillator and a trans-differentiation network. Copyright © 2017, The Authors. All rights reserved.

关键词： Stochastic systems

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Nanoantenna-microcavity hybrids with highly cooperative plasmonic-photonic coupling

arXiv

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arXiv 2017年

作者： Liu, Jui-Nung Huang, Qinglan Liu, Keng-Ku Singamaneni, Srikanth Cunningham, Brian T. Department of Electrical and Computer Engineering Department of Bioengineering Micro and Nanotechnology Laboratory University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Engineering and Materials Science Institute of Materials Science and Engineering Washington University in St. Louis St. LouisMO63130 United States

Nanoantennas offer the ultimate spatial control over light by concentrating optical energy well below the diffraction limit, whereas their quality factor (Q) is constrained by large radiative and dissipative losses. Dielectric microcavities, on the other hand, are capable of generating a high Qfactor through an extended photon storage time, but have a diffraction-limited optical mode volume. Here we bridge the two worlds, by studying an exemplary hybrid system integrating plasmonic gold nanorods acting as nanoantennas with an on-resonance dielectric photonic crystal (PC) slab acting as a low-loss microcavity, and, more importantly, by synergistically combining their advantages to produce a much stronger local field enhancement than that of the separate entities. To achieve this synergy between the two polar opposite types of nanophotonic resonant elements, we show that it is crucial to coordinate both the dissipative loss of the nanoantenna and the Q-factor of the low-loss cavity. In comparison to the antenna−cavity coupling approach using a Fabry−Perot resonator, which has proved successful for resonant amplification of the antenna's local field intensity, we theoretically and experimentally show that coupling to a modest-Q PC guided resonance can produce a greater amplification by at least an order of magnitude. The synergistic nanoantenna−microcavity hybrid strategy opens new opportunities for further enhancing nanoscale light-matter interactions to benefit numerous areas such as nonlinear optics, nanolasers, plasmonic hot carrier technology, and surface-enhanced Raman and infrared absorption spectroscopies. Copyright © 2017, The Authors. All rights reserved.

关键词： Plasmonics

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Quantum computing at the frontiers of biological sciences

arXiv

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arXiv 2019年

作者： Emani, Prashant S. Warrell, Jonathan Anticevic, Alan Bekiranov, Stefan Gandal, Michael McConnell, Michael J. Sapiro, Guillermo Aspuru-Guzik, Alán Baker, Justin Bastiani, Matteo McClure, Patrick Murray, John Sotiropoulos, Stamatios N. Taylor, Jacob Senthil, Geetha Lehner, Thomas Gerstein, Mark B. Harrow, Aram W. Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Yale School of Medicine Department of Psychiatry New HavenCT06511 United States University of Virginia School of Medicine Department of Biochemistry and Molecular Genetics CharlottesvilleVA22903 United States Department of Psychiatry Semel Institute David Geffen School of Medicine University of California–Los Angeles 695 Charles E. Young Drive South Los AngelesCA90095 United States Univ. of Virginia School of Medicine Department of Neuroscience CharlottesvilleVA22903 United States Department of Electrical and Computer Engineering Duke University DurhamNC27708 United States Department of Chemistry University of Toronto 80 St. George Street TorontoONM5S 3H6 Canada TorontoONM5S 1M1 Canada CIFAR Artificial Intelligence Research Chair Vector Institute TorontoONM5S 1M1 Canada Department of Computer Science University of Toronto 40 St. George Street TorontoONM5S 2E4 Canada Schizophrenia and Bipolar Disorder Program McLean Hospital BelmontMA02478 United States Department of Psychiatry Harvard Medical School BostonMA02114 United States Sir Peter Mansfield Imaging Centre School of Medicine University of Nottingham NottinghamNG7 2RD United Kingdom Machine Learning Team National Institute of Mental Health BethesdaMD20892 United States Section on Functional Imaging Methods National Institute of Mental Health BethesdaMD20892 United States Department of Psychiatry Yale University School of Medicine New HavenCT06511 United States Department of Physics Yale University New HavenCT06511 United States Joint Center for Quantum Information and Computer Science University of Maryland College ParkMD20742 United States National Institute of Standards and Technology GaithersburgMD20899 United States Office of Genomics Research Coordination N

The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems. Innovation in massively parallel, classical computing hardware and algorithms continues to address many of these challenges, but there is a need to simultaneously consider new paradigms to circumvent current barriers to processing speed. Accordingly, we articulate a view towards quantum computation and quantum information science, where algorithms have demonstrated potential polynomial and exponential computational speedups in certain applications, such as machine learning. The maturation of the field of quantum computing, in hardware and algorithm development, also coincides with the growth of several collaborative efforts to address questions across length and time scales, and scientific disciplines. We use this coincidence to explore the potential for quantum computing to aid in one such endeavor: the merging of insights from genetics, genomics, neuroimaging and behavioral phenotyping. By examining joint opportunities for computational innovation across fields, we highlight the need for a common language between biological data analysis and quantum computing. Ultimately, we consider current and future prospects for the employment of quantum computing algorithms in the biological sciences. Copyright © 2019, The Authors. All rights reserved.

关键词： Machine learning

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Author Correction: π-HuB: the proteomic navigator of the human body

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Nature 2025年第8046期637卷 E22页

作者： Fuchu He Ruedi Aebersold Mark S Baker Xiuwu Bian Xiaochen Bo Daniel W Chan Cheng Chang Luonan Chen Xiangmei Chen Yu-Ju Chen Heping Cheng Ben C Collins Fernando Corrales Jürgen Cox Weinan E Jennifer E Van Eyk Jia Fan Pouya Faridi Daniel Figeys George Fu Gao Wen Gao Zu-Hua Gao Keisuke Goda Wilson Wen Bin Goh Dongfeng Gu Changjiang Guo Tiannan Guo Yuezhong He Albert J R Heck Henning Hermjakob Tony Hunter Narayanan Gopalakrishna Iyer Ying Jiang Connie R Jimenez Lokesh Joshi Neil L Kelleher Ming Li Yang Li Qingsong Lin Cui Hua Liu Fan Liu Guang-Hui Liu Yansheng Liu Zhihua Liu Teck Yew Low Ben Lu Matthias Mann Anming Meng Robert L Moritz Edouard Nice Guang Ning Gilbert S Omenn Christopher M Overall Giuseppe Palmisano Yaojin Peng Charles Pineau Terence Chuen Wai Poon Anthony W Purcell Jie Qiao Roger R Reddel Phillip J Robinson Paola Roncada Chris Sander Jiahao Sha Erwei Song Sanjeeva Srivastava Aihua Sun Siu Kwan Sze Chao Tang Liujun Tang Ruijun Tian Juan Antonio Vizcaíno Chanjuan Wang Chen Wang Xiaowen Wang Xinxing Wang Yan Wang Tobias Weiss Mathias Wilhelm Robert Winkler Bernd Wollscheid Limsoon Wong Linhai Xie Wei Xie Tao Xu Tianhao Xu Liying Yan Jing Yang Xiao Yang John Yates Tao Yun Qiwei Zhai Bing Zhang Hui Zhang Lihua Zhang Lingqiang Zhang Pingwen Zhang Yukui Zhang Yu Zi Zheng Qing Zhong Yunping Zhu State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. hefc@***. International Academy of Phronesis Medicine (Guangdong) Guangdong China. hefc@***. Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland. aebersold@imsb.biol.ethz.ch. Macquarie Medical School Macquarie University Sydney New South Wales Australia. Institute of Pathology and Southwest Cancer Center Southwest Hospital Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology Ministry of Education of China Chongqing China. Institute of Health Service and Transfusion Medicine Beijing China. Department of Pathology and The Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University Baltimore MD USA. State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. Key Laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai China. Department of Nephrology First Medical Center of Chinese PLA General Hospital Nephrology Institute of the Chinese People's Liberation Army State Key Laboratory of Kidney Diseases National Clinical Research Center for Kidney Diseases Beijing Key Laboratory of Kidney Disease Research Beijing China. Institute of Chemistry Academia Sinica Taipei China. National Biomedical Imaging Center State Key Laboratory of Membrane Biology Institute of Molecular Medicine Peking-Tsinghua Center for Life Sciences College of Future Technology Peking University Beijing China. School of Biological Sciences Queen's University of Belfast Belfast UK. Functional Proteomics Laboratory Centro Nacional de Biotecnología-CSIC Madrid Spain. Computational Systems Biochemistry Research Group Ma

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Zinc‐Based Flow Batteries: Advanced Materials for Zinc‐Based Flow Battery: Development and Challenge (Adv. Mater. 50/2019)

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Advanced Materials 2019年第50期31卷

作者： Zhizhang Yuan Yanbin Yin Congxin Xie Huamin Zhang Yan Yao Xianfeng Li Division of Energy Storage Dalian National Laboratory for Clean Energy Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China Collaborative Innovation Center of Chemistry for Energy Materials (iChEM) Dalian 116023 P. R. China Department of Electrical and Computer Engineering and Materials Science and Engineering Program University of Houston Houston TX 77204 USA

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electrical tuning of the polarization state of light using graphene-integrated anisotropic metasurfaces

Electrical tuning of the polarization state of light using g...

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作者： Dutta-Gupta, Shourya Dabidian, Nima Kholmanov, Iskandar Belkin, Mikhail A. Shvets, Gennady Department of Physics Center for Nano and Molecular Science and Technology University of Texas at Austin AustinTX78712 United States Department of Mechanical Engineering Materials Science Program University of Texas at Austin AustinTX78712 United States Department of Electrical and Computer Engineering Microelectronics Research Center University of Texas at Austin 10100 Burnet Road AustinTX78758 United States CNR-INO Sensor Lab University of Brescia via Branze 45 Brescia25123 Italy School of Applied and Engineering Physics Cornell University IthacaNY14853 United States

Plasmonic metasurfaces have been employed for moulding the flow of transmitted and reflected light, thereby enabling numerous applications that benefit from their ultra-thin sub-wavelength format. Their appeal is further enhanced by the incorporation of active electro-optic elements, paving the way for dynamic control of light's properties. In this paper, we realize a dynamic polarization state generator using a graphene-integrated anisotropic metasurface (GIAM) that converts the linear polarization of the incident light into an elliptical one. This is accomplished by using an anisotropic metasurface with two principal polarization axes, one of which possesses a Fano-type resonance. A gate-controlled single-layer graphene integrated with the metasurface was employed as an electro-optic element controlling the phase and intensity of light polarized along the resonant axis of the GIAM. When the incident light is polarized at an angle to the resonant axis of the metasurface, the ellipticity of the reflected light can be dynamically controlled by the application of a gate voltage. Thus accomplished dynamic polarization control is experimentally demonstrated and characterized bymeasuring the Stokes polarization parameters. Large changes of the ellipticity and the tilt angle of the polarization ellipse are observed. Our measurements show that the tilt angle can be changed from positive values through zero to negative values while keeping the ellipticity constant, potentially paving the way to rapid ellipsometry and other characterization techniques requiring fast polarization shifting. This article is part of the themed issue 'New horizons for nanophotonics'. © 2017 The Author(s) Published by the Royal Society. All rights reserved.

关键词： Graphene

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Total variation superiorized conjugate gradient method for image reconstruction

arXiv

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arXiv 2017年

作者： Zibetti, Marcelo V. W. Lin, Chuan Herman, Gabor T. Graduate Program in Electrical Engineering and Computer Science Federal University of Technology - Paraná Curitiba80230-901 Brazil School of Electrical Engineering Southwest Jiaotong University Chengdu Sichuan610031 China Department of Computer Science Graduate Center City University of New York New YorkNY10016 United States

The conjugate gradient (CG) method is commonly used for the relatively-rapid solution of least squares problems. In image reconstruction, the problem can be ill-posed and also contaminated by noise;due to this, approaches such as regularization should be utilized. Total variation (TV) is a useful regularization penalty, frequently utilized in image reconstruction for generating images with sharp edges. When a non-quadratic norm is selected for regularization, as is the case for TV, then it is no longer possible to use CG. Nonlinear CG is an alternative, but it does not share the efficiency that CG shows with least squares and methods such as fast iterative shrinkage-thresholding algorithms (FISTA) are preferred for problems with TV norm. A different approach to including prior information is superiorization. In this paper it is shown that the conjugate gradient method can be superiorized. Five different CG variants are proposed, including preconditioned CG. The CG methods superiorized by the total variation norm are presented and their performance in image reconstruction is demonstrated. It is illustrated that some of the proposed variants of the superiorized CG method can produce reconstructions of superior quality to those produced by FISTA and in less computational time, due to the speed of the original CG for least squares problems. In the Appendix we examine the behavior of one of the superiorized CG methods (we call it S-CG);one of its input parameters is a positive number ". It is proved that, for any given " that is greater than the half-squared-residual for the least squares solution, S-CG terminates in a finite number of steps with an output for which the half-squared-residual is less than or equal to ". Importantly, it is also the case that the output will have a lower value of TV than what would be provided by unsuperiorized CG for the same value " of the half-squared residual. Copyright © 2017, The Authors. All rights reserved.

关键词： Conjugate gradient method

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Augmented Reality for Presenting Local Wisdom: Sumatera Utara Traditional House

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Journal of Physics: Conference Series 2019年第1期1235卷

作者： M F Syahputra R Aulia O S Sitompul U Andayani D Abdullah S Sriadhi R F Nanuru M D Utama R T Manurung H Djanggih E Mouw Department of Information Technology Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Utara Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Universitas Kristen Indonesia Maluku Ambon Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Faculty of Law Universitas Tompotika Luwuk Banggai Indonesia Faculty of Social and Human Sciences Universitas Halmahera Indonesia

Augmented Reality is a technology that allows users to see the real world, with virtual objects placed on it or combined with the real world. Augmented Reality itself can be applied to various things, including as an educational media. In the field of education, technology can be used a culture introduction to society. One part of Indonesian culture is traditional houses. Traditional house is a building that symbolizes the culture of the local community. In North Sumatra itself, there are several traditional houses that have different forms. The use of Vuforia SDK in the construction of this application can display augmented objects in the form of 3-dimentional objects and also provide information on the house. This application will run on the Android mobile platform to make it easier for users to access it. In addition, users can choose their own objects to be used as markers to make the application use much easier.

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Intrinsic Raman signatures of pristine hybrid perovskite CH3NH3PbI3 and its multiple stages of structure transformation 44

Intrinsic Raman signatures of pristine hybrid perovskite CH3...

引用

44th IEEE Photovoltaic Specialist Conference, PVSC 2017

作者： Chen, Qiong Liu, Henan Kim, Hui-Seon Liu, Yucheng Yang, Mengjin Yue, Naili Ren, Gang Zhu, Kai Liu, Shengzhong Frank Park, Nam-Gyu Zhang, Yong Department of Electrical and Computer Engineering Korea Republic of Optical Science and Engineering Graduate Program University of North Carolina at Charlotte CharlotteNC28223 United States School of Chemical Engineering and Department of Energy Science Sungkyunkwan University Suwon440-746 Korea Republic of Key Laboratory of Applied Surface and Colloid Chemistry National Ministry of EducationInstitute for Advanced Energy Materials School of Materials Science and Engineering Shaanxi Normal University Xi'an710062 China Chemical and Materials Science Center National Renewable Energy Laboratory GoldenCO80401 United States Molecular Foundry Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

ISBN: (纸本)9781509056057

By performing spatially resolved Raman and photoluminescence spectroscopy with different illumination conditions, we have achieved a unified understanding towards the spectroscopy signatures of the organic-inorganic hybrid perovskite, transforming from the pristine state (CH3NH3PbI3 or MAPbI3) to fully degraded state (i.e., PbI2), for samples with varying crystalline domain size from mesoscopic scale to macroscopic size, synthesized by three different techniques. © 2017 IEEE.

关键词： Perovskite

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Stochastic geometry model for multi-channel fog radio access networks

Stochastic geometry model for multi-channel fog radio access...

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International Symposium on Modeling and Optimization in Mobile, Ad Hoc, and Wireless Networks (WiOpt)

作者： Mostafa Emara Hesham ElSawy Sameh Sorour Samir Al-Ghadhban Mohamed-Slim Alouini Tareq Y. Al-Naffouri Department of Electrical Engineering King Fahd University of Petroleum and Minerals (KFUPM) Saudi Arabia King Abdullah University of Science and Technology Thuwal SA Department of Electrical and Computer Engineering University of Idaho USA CEMSE Division EE program King Abdullah University of Science and Technology (KAUST) Saudi Arabia

ISBN: (纸本)9781509047109

Cache-enabled base station (BS) densification, denoted as a fog radio access network (F-RAN), is foreseen as a key component of 5G cellular networks. F-RAN enables storing popular files at the network edge (i.e., BS caches), which empowers local communication and alleviates traffic congestions at the core/backhaul network. The hitting probability, which is the probability of successfully transmitting popular files request from the network edge, is a fundamental key performance indicator (KPI) for F-RAN. This paper develops a scheduling aware mathematical framework, based on stochastic geometry, to characterize the hitting probability of F-RAN in a multi-channel environment. To this end, we assess and compare the performance of two caching distribution schemes, namely, uniform caching and Zipf caching. The numerical results show that the commonly used single channel environment leads to pessimistic assessment for the hitting probability of F-RAN. Furthermore, the numerical results manifest the superiority of the Zipf caching scheme and quantify the hitting probability gains in terms of the number of channels and cache size.

关键词： Stochastic processes Mathematical model Geometry Interference Cellular networks Numerical models Conferences

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