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Electronic Excitations in Complex Molecular Environments: Many-Body Green’s Functions Theory in VOTCA-XTP

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arXiv 2018年

作者： Wehner, Jens Brombacher, Lothar Brown, Joshua Junghans, Christoph Çaylak, Onur Khalak, Yuriy Madhikar, Pranav Tirimbò, Gianluca Baumeier, Björn Max Planck Institute for Polymer Research Ackermannweg 10 MainzD-55128 Germany Eindhoven University of Technology Department of Mathematics and Computer Science & Institute for Complex Molecular Systems P.O. Box 513 Eindhoven5600MB Netherlands Dept. of Electrical Computer and Energy Engineering University of Colorado Boulder 425 UCB BoulderCO80309 United States Renewable and Sustainable Energy Institute University of Colorado Boulder 4001 Discovery Dr BoulderCO80303 United States Computer Computational and Statistical Sciences Division Los Alamos National Laboratory Los AlamosNM87545 United States Eindhoven University of Technology Department of Mathematics and Computer Science & Institute for Complex Molecular Systems P.O. Box 513 Eindhoven5600MB Netherlands

Many-body Green’s functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identify techniques, the code is designed specifically for non-periodic systems. Application to the small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2-8 eV in single molecules. Further, embedding each GW -BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW -BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an inital (fast) decay of such an UV excited state into a bi-nucleobase CT exciton. The results show that VOTCA-XTP’s GW -BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments. Copyright © 2018, The Authors. All rights reserved.

关键词： Quantum chemistry

REFUGE Challenge: A unified framework for evaluating automated methods for glaucoma assessment from fundus photographs

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arXiv 2019年

作者： Orlando, Jose Ignacio Fu, Huazhu Breda, Jo-Ao Barbossa Keer, Karelvan Bathula, Deepti R. Diaz-Pinto, Andres Fang, Ruogu Heng, Pheng-Ann Kim, Jeyoung Lee, JoonHo Lee, Joonseok Li, Xiaoxiao Liu, Peng Lu, Shuai Murugesan, Balamurali Naranjo, Valery Phaye, Sai Samarth R. Shankaranarayana, Sharath M. Sikka, Apoorva Son, Jaemin Hengel, Antonvanden Wang, Shujun Wu, Junyan Wu, Zifeng Xu, Guanghui Xu, Yongli Yin, Pengshuai Li, Fei Zhang, Xiulan Xu, Yanwu Bogunovic, Hrvoje Department of Ophthalmology and Optometry Medical University of Vienna Spitalgasse 23 Vienna1090 Australia Inception Institute of Artificial Intelligence Abu Dhabi United Arab Emirates Surgery and Physiology Department Ophthalmology Unit Faculty of Medicine University of Porto Porto Research Group Ophthalmology KU Leuven Leuven Belgium Ropar Rupnagar140001 India Instituto de Investigacione Innovacion en Bioingeniera Universitat Politecnica de Valencia Valencia46022 Spain J. Crayton Pruitt Family Dept. of Biomedical Engineering University of Florida 32611 United States Department of Computer Science and Engineering Chinese University of Hong Kong 999077 Hong Kong Gachon University Gyeonggi-Do461-701 Korea Republic of Samsung SDS AI Research Center Seoul06765 Korea Republic of Yale University New HavenCT06510 United States Faculty of Science Beijing University of Chemical Technology Beijing100029 China Healthcare Technology Innovation Centre IIT Madras India Department of Electrical Engineering IIT Madras India VUNO Inc Seoul137-810 Korea Republic of Australian Institute for Machine Learning Australia Cleerly Inc New YorkNY10022 United States South China University of Technology Guangzhou510006 China Zhongshan Ophthalmic Center Sun Yat-sen University Guangzhou Shi China Articial Intelligence Innovation Business Baidu Inc China and Cixi Institute of Bio Medical Engineering Chinese Academy of Sciences China

Glaucoma is one of the leading causes of irreversible but preventable blindness in working age populations. Color fundus photography (CFP) is the most cost-effective imaging modality to screen for retinal disorders. However, its application to glaucoma has been limited to the computation of a few related biomarkers such as the vertical cup-to-disc ratio. Deep learning approaches, although widely applied for medical image analysis, have not been extensively used for glaucoma assessment due to the limited size of the available data sets. Furthermore, the lack of a standardize benchmark strategy makes dificult to compare existing methods in a uniform way. In order to overcome these issues we set up the Retinal Fundus Glaucoma Challenge, REFUGE (http://***), held in conjunction with MICCAI 2018. The challenge consistedof two primary tasks, namely optic disc/cup segmentation and glaucoma classification. As part of REFUGE, we have publicly released a data set of 1200 fundus images with ground truth segmentations and clinical glaucoma labels, currently the largest existing one. We have also built an evaluation framework to ease and ensure fairness in the comparison of different models, encouraging the development of novel techniques in the field. 12 teams qualified and participated in the online challenge. This paper summarizes their methods and analyzes their corresponding results. In particular, we observed that two of the top-ranked teams outperformed two human experts in the glaucoma classification task. Furthermore, the segmentation results were in general consistent with the ground truth annotations, with complementary outcomes that can be further exploited by ensembling the results. Copyright © 2019, arXiv, All rights reserved.

关键词： Ophthalmology

Polyp Segmentation in Colonoscopy Images Using Fully Convolutional Network

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arXiv 2018年

作者： Akbari, Mojtaba Mohrekesh, Majid Nasr-Esfahani, Ebrahim Soroushmehr, S.M. Reza Karimi, Nader Samavi, Shadrokh Najarian, Kayvan Department of Electrical and Computer Engineering Isfahan University of Technology Isfahan84156-83111 Iran Dept. of Compl. Med. and Bioinfo. and Michigan Center for Integrative Research in Critical Care University of Michigan Ann Arbor United States Department of Emergency Medicine University of Michigan Ann Arbor U.S.A. United States Department of Emergency Medicine and Michigan Center for Integrative Research in Critical Care Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor United States

Colorectal cancer is a one of the highest causes of cancer-related death, especially in men. Polyps are one of the main causes of colorectal cancer and early diagnosis of polyps by colonoscopy could result in successful treatment. Diagnosis of polyps in colonoscopy videos is a challenging task due to variations in the size and shape of polyps. In this paper we proposed a polyp segmentation method based on convolutional neural network. Performance of the method is enhanced by two strategies. First, we perform a novel image patch selection method in the training phase of the network. Second, in the test phase, we perform an effective post processing on the probability map that is produced by the network. Evaluation of the proposed method using the CVC-ColonDB database shows that our proposed method achieves more accurate results in comparison with previous colonoscopy video-segmentation methods. Copyright © 2018, The Authors. All rights reserved.

关键词： Endoscopy

The sounds of science – A symphony for many instruments and voices

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arXiv 2019年

作者： Alexander, Gerianne Allen, Roland E. Atala, Anthony Bowen, Warwick P. Coley, Alan A. Goodenough, John Katsnelson, Mikhail I. Koonin, Eugene V. Krenn, Mario Madsen, Lars S. Månsson, Martin Mauranyapin, Nicolas P. Melvin, Art I. Rasel, Ernst Reichl, Linda E. Yampolskiy, Roman Yasskin, Philip B. Zeilinger, Anton Lidström, Suzy Department of Psychological and Brain Sciences Texas A&M University College StationTX United States Department of Physics and Astronomy Texas A&M University College StationTX United States Wake Forest Institute for Regenerative Medicine 391 Technology Way Winston-SalemNC27157 United States School of Mathematics and Physics University of Queensland St. Lucia4072 Australia Australian Centre for Engineered Quantum Systems University of Queensland St. Lucia4072 Australia Department of Mathematics and Statistics Dalhousie University HalifaxNSB3H 4R2 Canada Walker Department of Mechanical Engineering Cockrell Institute University of Texas at Austin AustinTX United States Institute for Molecules and Materials Radboud University Nijmegen6525AJ Netherlands National Library of Medicine National Center for Biotechnology Information BethesdaMD20894 United States Austrian Academy of Sciences Boltzmanngasse 3 Vienna1090 Austria Department of Chemistry University of Toronto Toronto Canada Dept. of Applied Physics KTH Royal Institute of Technology Stockholm KistaSE-164 40 Sweden Faculty of Physics University of Vienna Boltzmanngasse 5 Vienna1090 Austria Institut für Quantenoptik Welfengarten 1 Hannover30167 Germany Center for Complex Quantum Systems Department of Physics University of Texas at Austin AustinTX United States Department of Computer Engineering and Computer Science Duthie Center for Engineering University of Louisville LouisvilleKY40292 United States Department of Mathematics Texas A&M University College StationTX United States Department of Physics and Astronomy Texas A&M University College StationTX United States

Sounds of Science is the first movement of a symphony for many (scientific) instruments and voices, united in celebration of the frontiers of science. John Goodenough, the maestro who transformed energy usage and technology through the invention of the lithium-ion battery, opens the programme, reflecting on the ultimate limits of battery technology. This applied theme continues through the subsequent pieces on energy related topics – the sodium-ion battery and artificial fuels, by Martin Månsson – and the ultimate challenge for 3D printing, the eventual production of life, by Anthony Atala. A passage by Gerianne Alexander follows, reflecting on a related issue: How might an artificially produced human being behave? Next comes a consideration of consiousness and free will by Roland Allen and Suzy Lidström. Further voices and new instruments enter as Warwick Bowen, Nicolas Mauranyapin and Lars Madsen discuss whether dynamical processes of single molecules might be observed in their native state. The exploitation of chaos in science and technology, applications of Bose-Einstein condensates and a consideration of the significance of entropy follow in pieces by Linda Reichl, Ernst Rasel and Roland Allen, respectively. Mikhail Katsnelson and Eugene Koonin then discuss the potential generalisation of thermodynamic concepts in the context of biological evolution. Entering with the music of the cosmos, Philip Yasskin discusses whether we might be able to observe torsion in the geometry of the universe. The crescendo comes with the crisis of singularities, their nature and whether they can be resolved through quantum effects, in the composition of Alan Coley. The climax is Mario Krenn, Art Melvin and Anton Zeilinger’s consideration of how computer code can be autonomously surprising and creative. In a harmonious counterpoint – his ‘Guidelines for considering AIs as coauthors’ – Roman Yampolskiy concludes that such code is not yet able to take responsibility for coauthoring a

关键词： Metal ions

A framework for OpenFlow-like Policy-based routing in hybrid software defined networks 11

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A framework for OpenFlow-like Policy-based routing in hybrid...

11th International Network Conference, INC 2016

作者： Mishra, Anshuman Bansod, Deven Haribabu, K. Dept. of Electrical and Electronics Engineering Birla Institute of Technology and Science Pilani India Dept. of Computer Science and Information Systems Birla Institute of Technology and Science Pilani India

ISBN: (纸本)9781841024103

Software Defined Networks (SDNs) provide a centralized view and allow extensive programmability of the network. They separate the control and data planes opening up immense scope in developing low cost control and management applications to operate the network. Yet, network administrators are ambivalent to revamp their entire network hardware to bring in SDN-compatible switches. This leads to the need for developing models for gradual adaptation of SDN technology. In this paper, we present a framework which allows for policy implementations based on all OpenFlow version 1.4 specified match fields, over legacy Layer 3 devices. This would enable the legacy networks to reap the benefits of SDN in an incremental, controlled and consistent manner.

关键词： Software defined networking

A local universe host for the repeating fast radio burst FRB 20181030A

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arXiv 2021年

作者： Bhardwaj, Mohit Kirichenko, A.Y. Michilli, D. Mayya, Y.D. Kaspi, V.M. Gaensler, B.M. Rahman, M. Tendulkar, S.P. Fonseca, E. Josephy, Alexander Leung, C. Merryfield, Marcus Petroff, Emily Pleunis, Z. Sanghavi, Pranav Scholz, P. Shin, K. Smith, Kendrick M. Stairs, I.H. Department of Physics McGill University 3600 rue University MontréalQCH3A 2T8 Canada McGill Space Institute McGill University 3550 rue University MontréalQCH3A 2A7 Canada Instituto de Astronomía Universidad Nacional Autónoma de México Apdo. Postal 877 Baja California Ensenada22800 Mexico Ioffe Institute 26 Politekhnicheskaya st. St. Petersburg194021 Russia Instituto Nacional de Astrofísica Óptica y Electrónica Luis Enrique Erro 1 Tonantzintla Puebla72840 Mexico Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Department of Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Sidrat Research PO Box 73527 RPO Wychwood TorontoONM6C 4A7 Canada Department of Astronomy and Astrophysics Tata Institute of Fundamental Research Mumbai400005 India National Centre for Radio Astrophysics Post Bag 3 Ganeshkhind Pune411007 India MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Department of Physics Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Lane Department of Computer Science and Electrical Engineering 1220 Evansdale Drive PO Box 6109 MorgantownWV26506 United States Center for Gravitational Waves and Cosmology West Virginia University Chestnut Ridge Research Building MorgantownWV26505 United States Perimeter Institute for Theoretical Physics 31 Caroline Street N WaterlooONN25 2YL Canada Dept. of Physics and Astronomy 6224 Agricultural Road VancouverBCV6T 1Z1 Canada

We report on the host association of FRB 20181030A, a repeating fast radio burst (FRB) with a low dispersion measure (DM, 103.5 pc cm−3) discovered by CHIME/FRB Collaboration et al. (2019a). Using baseband voltage data saved for its repeat bursts, we localize the FRB to a sky area of 5.3 sq. arcmin (90% confidence). Within the FRB localization region, we identify NGC 3252 as the most promising host, with an estimated chance coincidence probability −3. Moreover, we do not find any other galaxy with Mr 26erg s−1Hz−1, at least 1500 times smaller than that of the FRB 20121102A persistent radio source. We also argue that a population of young millisecond magnetars alone cannot explain the observed volumetric rate of repeating FRBs. Finally, FRB 20181030A is a promising source for constraining FRB emission models due to its proximity, and we strongly encourage its multi-wavelength follow-up. Copyright © 2021, The Authors. All rights reserved.

关键词： Galaxies

Blind multiclass ensemble classification

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arXiv 2017年

作者： Traganitis, Panagiotis A. Pagès-Zamora, Alba Giannakis, Georgios B. Dept. of Electrical and Computer Engineering and the Digital Technology Center University of Minnesota MinneapolisMN55455 United States SPCOM Group Universitat Politècnica de Catalunya BarcelonaTech Spain

The rising interest in pattern recognition and data analytics has spurred the development of innovative machine learning algorithms and tools. However, as each algorithm has its strengths and limitations, one is motivated to judiciously fuse multiple algorithms in order to find the "best" performing one, for a given dataset. Ensemble learning aims at such high-performance meta-algorithm, by combining the outputs from multiple algorithms. The present work introduces a blind scheme for learning from ensembles of classifiers, using a moment matching method that leverages joint tensor and matrix factorization. Blind refers to the combiner who has no knowledge of the ground-truth labels that each classifier has been trained on. A rigorous performance analysis is derived and the proposed scheme is evaluated on synthetic and real datasets. Copyright © 2017, The Authors. All rights reserved.

关键词： Crowdsourcing

A new sensitivity approach in multi-objective design: An application in electromechanics 18

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A new sensitivity approach in multi-objective design: An app...

18th International Symposium on Electromagnetic Fields in Mechatronics, electrical and Electronic engineering, ISEF 2017

作者： Di Barba, Paolo Mognaschi, Maria Evelina Lowther, David Alister Wiak, Stawomir Dept. of Electrical Computer and Biomedical Engineering University of Pavia Pavia Italy McGill University Montreal Canada Inst. of Mechatronics and Information Systems Lódź University of Technology Lódź Poland

ISBN: (纸本)9781538616611

In the paper, a new approach to the robust optimal design is proposed. The idea is to consider the sensitivity as an extra objective function which is cost-effective. The optimal design of a switched-reluctance motor is considered as the case study: since the case study exhibits two design criteria, the Pareto front trading off three objective functions is approximated by means of evolutionary computing. © 2017 IEEE.

关键词： Finite element method

Implementation of PID posture controller for 6 DOF underwater robot 15

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Implementation of PID posture controller for 6 DOF underwate...

15th International Conference on Electronics, Information, and Communications, ICEIC 2016

作者： Ariyachartphadungkit, Teeratath Vanijjirattikhan, Rangsarit Hasegawa, Shoichi Dept. of Electrical Engineering Faculty of Engineering Kasetsart University Bangkok Thailand National Electronics and Computer Technology Center Pathumthani Thailand Tokyo Institute of Technology Japan

ISBN: (纸本)9781467380164

An underwater robot is widely used in many industries. The posture control of the robot is importance since it makes a robot able to move in hard environment with stability and precision to the desired locations. The designed underwater robot consists of 8 custom made thrusters in order control all robot state variables and make the motion achieve 6 Degrees-Of-Freedom. Newtonian method is used to model the dynamics of the underwater robot. Nonlinearity of the robot dynamics is suppressed by feedback linearization method with proper parameters. Discrete Proportional-Integral-Derivative (PID) controller is used as the thruster controller and also the robot posture controller. The experiments are conducted and all the robot controller gains are tuned. The experimental results show that PID controller can control robot postures with robustness. © 2016 IEEE.

关键词： Three term control systems