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Teaching computational reproducibility for neuroimaging

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arXiv 2018年

作者： Jarrod Millman, K. Brett, Matthew Barnowski, Ross Poline, Jean-Baptiste Division of Biostatistics UC Berkeley BerkeleyCA United States Berkeley Institute for Data Science UC Berkeley BerkeleyCA United States College of Life and Environmental Sciences University of Birmingham Birmingham United Kingdom Applied Nuclear Physics Program Lawrence Berkeley National Laboratory BerkeleyCA United States Neurology and Neurosurgery McGill University MontrealQC Canada

We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MRI scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science. Copyright © 2018, The Authors. All rights reserved.

关键词： Students

Scattering of a short electromagnetic pulse from a Lorentz-Duffing film: Theoretical and numerical analysis

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arXiv 2018年

作者： Brio, Moysey Caputo, Jean-Guy Gwirtz, Kyle Liu, Jinjie Maimistov, Andrei Department of Mathematics University of Arizona TucsonAZ85721 United States Laboratoire de Mathématiques INSA Rouen Normandie Saint-Etienne du Rouvray76801 France Program in Applied Mathematics University of Arizona TucsonAZ85721 United States Department of Mathematical Sciences Delaware State University DoverDE19901 United States Department of Solid State Physics and Nanostructures National Research Nuclear University Moscow Engineering Physics Institute Kashirskoe sh. 31 Moscow115409 Russia

We combine scattering theory, Fourier, traveling wave and asymptotic analyses together with numerical simulations to present interesting and practically useful properties of femtosecond pulse interaction with thin films. The dispersive material is described by a single resonance Lorentz model and its nonlinear extension with a cubic Duffing-type nonlinearity. A key feature of the Lorentz dielectric function is that its real part becomes negative between its zero and its pole, generating a forbidden region. We illustrate numerically the linear interaction of the pulse with the film using both scattering theory and Fourier analysis. Outside this region we show the generation of a sequence of pulses separated by round trips in the Fabry-Perot cavity due to multiple reflections. When the pulse spectrum is inside the forbidden region, we observe total reflection. Near the pole of the dielectric function, we demonstrate the slowing down of the pulse (group velocity tending to zero) in the medium that behaves as a high-Q cavity. We use the combination of analysis and simulations in the linear regime to validate the delta function approximation of the thin layer;this collapses the forbidden region to a single resonant point of the spectrum. We also study the single cycle pulse interaction with a thin film and show three distinct types of reflection: half-pulse, sinusoidal wave train and cosine wavelet. Finally we analyze the influence of a strong nonlinearity and observe that the film switches from reflecting to trasparent. Copyright © 2018, The Authors. All rights reserved.

关键词： Thin films

Polaronic quasiparticle picture for generation dynamics of coherent phonons in semiconductors: Transient and nonlinear Fano resonance

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Physical Review B 2017年第1期95卷 014301-014301页

作者： Yohei Watanabe Ken-ichi Hino Muneaki Hase Nobuya Maeshima Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Division of Materials Science Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba 305-8577 Japan Division of Applied Physics Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8573 Japan

We examine generation dynamics of coherent phonons in both polar and nonpolar semiconductors, such as GaAs and Si, based on a polaronic-quasiparticle (PQ) model. In this model, the PQ operator is composed of two kinds of operators: one is a quasiboson operator, defined as a linear combination of a set of pairs of electron operators, and the other is a longitudinal optical (LO) phonon operator. In particular, the problem of transient and nonlinear Fano resonance (FR) is tackled, where the vestige of this quantum interference effect was observed exclusively in lightly n-doped Si immediately after carriers were excited by an ultrashort pulse laser [M. Hase et al., Nature (London) 426, 51 (2003)], although not observed yet in GaAs. The PQ model enables us to show straightforwardly that the phonon energy state is embedded in continuum states formed by a set of adiabatic eigenstates of the quasiboson; this energy configuration is a necessary condition of the manifestation of the transient FR in the present optically nonlinear system. Numerical calculations are done for photoemission spectra relevant to the retarded longitudinal dielectric function of transient photoexcited states and for power spectra relevant to the LO-phonon displacement function of time. The photoemission spectra show that in undoped Si, an asymmetric spectral profile characteristic of FR comes into existence immediately after the instantaneous carrier excitation to fade out gradually, whereas in undoped GaAs, no asymmetry in spectra appears in the whole temporal region. The similar results are also obtained in the power spectra. These results are in harmony with the reported experimental results. It is found that the obtained difference in spectral profile between undoped Si and GaAs is attributed to a phase factor of an effective interaction between the LO phonon and the quasiboson. More detailed discussion of the FR dynamics is made in the text.

关键词： Optical phonons Polarons Ultrafast phenomena Elemental semiconductors Semiconductor compounds Semiconductors Linear response theory

Author Correction: Proton acceleration in thermonuclear nova explosions revealed by gamma rays

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Nature Astronomy 2022年 760页

作者： V. A. Acciari J. Becerra González E. Colombo R. J. García López J. Herrera A. López-Oramas C. Maggio V. Moreno M. Nievas Rosillo J. Otero-Santos G. Vanzo M. Vazquez Acosta S. Ansoldi B. De Lotto A. Donini F. Longo D. Miceli M. Palatiello M. Persic L. A. Antonelli C. Bigongiari S. Covino V. D’Elia F. Dazzi A. Lamastra F. Leone S. Lombardi L. Maraschi L. Nava S. Paiano C. Righi F. G. Saturni A. Stamerra F. Tavecchio A. Tutone A. Biland S. Fukami M. Artero O. Blanch S. M. Colak M. Delfino J. Delgado E. Do Souto Espiñeira L. Fariña Alonso L. Jouvin D. Kerszberg M. Martínez A. Moralejo E. Moretti C. Nigro C. Priyadarshi J. Rico K. Asano D. Hadasch M. Hütten T. Inada Y. Iwamura Y. Kobayashi D. Mazin K. Noda Y. Ohtani T. Saito S. Sakurai J. Sitarek M. Strzys M. Takahashi R. Takeishi M. Teshima I. Vovk D. Baack H. Bökenkamp D. Elsaesser A. Fattorini L. Linhoff S. Mender W. Rhode K. Schmidt A. Babić Ž. Bošnjak S. Cikota A. Baquero J. A. Barrio J. L. Contreras M. V. Fonseca J. Hoang M. López-Moya A. Mas Aguilar T. Miener D. Morcuende P. Peñil U. Barres de Almeida B. Machado de Oliveira Fraga I. Batković M. Bernardos G. Busetto A. De Angelis M. Doro R. López-Coto M. Mallamaci M. Mariotti E. Prandini A. Spolon W. Bednarek P. Gliwny K. Ishio D. Sobczynska L. Bellizzi S. Menchiari J. M. Miranda R. Paoletti S. Truzzi S. Ventura C. Wunderlich E. Bernardini W. Bhattacharyya M. Garczarczyk K. Satalecka A. Arbet Engels A. Berti J. Besenrieder G. Ceribella Y. Chai G. D’Amico C. Fruck J. G. Green D. Green A. Hahn L. Heckmann R. Mirzoyan D. Paneque M. Pihet T. Schweizer D. Strom J. van Scherpenberg M. Will G. Bonnoli R. Carosi P. Da Vela P. G. Prada Moroni A. Rugliancich M. Cerruti E. Molina J. M. Paredes M. Ribó A. Chilingarian J. Cortina C. Delgado Mendez T. Hassan I. Jiménez Martínez A. Del Popolo D. Depaoli F. Di Pierro C. F. Vigorito L. Di Venere N. Giglietto F. Giordano S. Loporchio D. Dominis Prester M. Manganaro S. Mićanović L. Pavletić T. Terzić D. Dorner K. Mannheim B. Schleicher V. Fallah Ramazani J. Jormanainen E. Lindfors Instituto de Astrofísica de Canarias and Dpto. de Astrofísica Universidad de La Laguna La Laguna Tenerife Spain Departament de Física and CERES-IEEC Universitat Autònoma de Barcelona Bellaterra Spain Università di Udine and INFN Trieste Udine Italy International Center for Relativistic Astrophysics (ICRA) Rome Italy Dipartimento di Fisica Università di Trieste Trieste Italy Laboratoire d’Annecy de Physique des Particules (LAPP) CNRS-IN2P3 Annecy Cedex France INAF Trieste and Dept. of Physics and Astronomy University of Bologna Bologna Italy National Institute for Astrophysics (INAF) Rome Italy ETH Zürich Zürich Switzerland Institut de Física d’Altes Energies (IFAE) The Barcelona Institute of Science and Technology (BIST) Bellaterra Barcelona Spain Port d’Informació Científica (PIC) Bellaterra Barcelona Spain Japanese MAGIC Group: Institute for Cosmic Ray Research (ICRR) The University of Tokyo Kashiwa Chiba Japan Max-Planck-Institut für Physik München Germany Technische Universität Dortmund Dortmund Germany Croatian MAGIC Group: University of Zagreb Faculty of Electrical Engineering and Computing (FER) Zagreb Croatia IPARCOS Institute and EMFTEL Department Universidad Complutense de Madrid Madrid Spain Department of Astronomy University of California Berkeley Berkeley CA USA Centro Brasileiro de Pesquisas Físicas (CBPF) Rio de Janeiro RJ Brazil Università di Padova and INFN Padova Italy University of Lodz Faculty of Physics and Applied Informatics Department of Astrophysics Lodz Poland Università di Siena and INFN Pisa Siena Italy Deutsches Elektronen-Synchrotron (DESY) Zeuthen Germany Department for Physics and Technology University of Bergen Bergen Norway Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n Granada Spain Università di Pisa and INFN Pisa Pisa Italy University of Innsbruck Innsbruck Austria Universitat de Barcelona ICCUB IEEC-UB Barcelona Spain Armenian MAGIC Group: A. Alikhanyan National Science Labo

Estimation of solar radiation using Angstrom-Prescott model and interpolation of empirical coefficients in Thailand

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Journal of physics: Conference Series 2018年第1期1144卷

作者： K Keawsang-in S Ratjiranukool P Ratjiranukool PhD's Degree Program in Applied Physics Faculty of Science Chiang Mai University Department of Physics and Materials Faculty of Science Chiang Mai University Department of Physics Faculty of Science and Technology Chiang Mai Rajabhat University

Angstrom-Prescott model, defined by , was applied to estimate solar L so J radiation for 11 meteorological stations in Thailand. In this research, the empirical coefficients ('a' and 'b') were calculated by using the least square model. Statistical values, i.e., root mean square error (RMSE) and correlation, were analyzed the model ability in estimating solar radiation by compared with the measurement. The empirical coefficients overall Thailand were interpolated by using geographic information system (GIS). This technique can be calculated for estimation of solar radiation in every region in Thailand. In the results, the statistical tests show the ability of Angstrom-Prescott model to estimate solar radiation in Thailand and the least square method is suitable for computing empirical coefficients.

关键词：

All-sky search for continuous gravitational waves from isolated neutron stars in the early O3 LIGO data

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Physical Review D 2021年第8期104卷 082004-082004页

作者： R. Abbott T. D. Abbott S. Abraham F. Acernese K. Ackley A. Adams C. Adams R. X. Adhikari V. B. Adya C. Affeldt D. Agarwal M. Agathos K. Agatsuma N. Aggarwal O. D. Aguiar L. Aiello A. Ain P. Ajith T. Akutsu K. M. Aleman G. Allen A. Allocca P. A. Altin A. Amato S. Anand A. Ananyeva S. B. Anderson W. G. Anderson M. Ando S. V. Angelova S. Ansoldi J. M. Antelis S. Antier S. Appert Koya Arai Koji Arai Y. Arai S. Araki A. Araya M. C. Araya J. S. Areeda M. Arène N. Aritomi N. Arnaud S. M. Aronson H. Asada Y. Asali G. Ashton Y. Aso S. M. Aston P. Astone F. Aubin P. Aufmuth K. AultONeal C. Austin S. Babak F. Badaracco M. K. M. Bader S. Bae Y. Bae A. M. Baer S. Bagnasco Y. Bai L. Baiotti J. Baird R. Bajpai M. Ball G. Ballardin S. W. Ballmer M. Bals A. Balsamo G. Baltus S. Banagiri D. Bankar R. S. Bankar J. C. Barayoga C. Barbieri B. C. Barish D. Barker P. Barneo F. Barone B. Barr L. Barsotti M. Barsuglia D. Barta J. Bartlett M. A. Barton I. Bartos R. Bassiri A. Basti M. Bawaj J. C. Bayley A. C. Baylor M. Bazzan B. Bécsy V. M. Bedakihale M. Bejger I. Belahcene V. Benedetto D. Beniwal M. G. Benjamin T. F. Bennett J. D. Bentley M. BenYaala F. Bergamin B. K. Berger S. Bernuzzi D. Bersanetti A. Bertolini J. Betzwieser R. Bhandare A. V. Bhandari D. Bhattacharjee S. Bhaumik J. Bidler I. A. Bilenko G. Billingsley R. Birney O. Birnholtz S. Biscans M. Bischi S. Biscoveanu A. Bisht B. Biswas M. Bitossi M.-A. Bizouard J. K. Blackburn J. Blackman C. D. Blair D. G. Blair R. M. Blair F. Bobba N. Bode M. Boer G. Bogaert M. Boldrini F. Bondu E. Bonilla R. Bonnand P. Booker B. A. Boom R. Bork V. Boschi N. Bose S. Bose V. Bossilkov V. Boudart Y. Bouffanais A. Bozzi C. Bradaschia P. R. Brady A. Bramley A. Branch M. Branchesi J. E. Brau M. Breschi T. Briant J. H. Briggs A. Brillet M. Brinkmann P. Brockill A. F. Brooks J. Brooks D. D. Brown S. Brunett G. Bruno R. Bruntz J. Bryant A. Buikema T. Bulik H. J. Bulten A. Buonanno R. Buscicchio D. Buskulic R. L. Byer L. Cadonati M. Caesar G. Cagnoli C. Cahillane H. W. Cain, III J. Calderón Bustillo J. LIGO Laboratory California Institute of Technology Pasadena California 91125 USA Louisiana State University Baton Rouge Louisiana 70803 USA Inter-University Centre for Astronomy and Astrophysics Pune 411007 India Dipartimento di Farmacia Università di Salerno I-84084 Fisciano Salerno Italy INFN Sezione di Napoli Complesso Universitario di Monte S.Angelo I-80126 Napoli Italy OzGrav School of Physics and Astronomy Monash University Clayton 3800 Victoria Australia Christopher Newport University Newport News Virginia 23606 USA LIGO Livingston Observatory Livingston Louisiana 70754 USA OzGrav Australian National University Canberra Australian Capital Territory 0200 Australia Max Planck Institute for Gravitational Physics (Albert Einstein Institute) D-30167 Hannover Germany Leibniz Universität Hannover D-30167 Hannover Germany University of Cambridge Cambridge CB2 1TN United Kingdom Theoretisch-Physikalisches Institut Friedrich-Schiller-Universität Jena D-07743 Jena Germany University of Birmingham Birmingham B15 2TT United Kingdom Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) Northwestern University Evanston Illinois 60208 USA Instituto Nacional de Pesquisas Espaciais 12227-010 São José dos Campos São Paulo Brazil Gravity Exploration Institute Cardiff University Cardiff CF24 3AA United Kingdom Gran Sasso Science Institute (GSSI) I-67100 L’Aquila Italy INFN Laboratori Nazionali del Gran Sasso I-67100 Assergi Italy INFN Sezione di Pisa I-56127 Pisa Italy Università di Pisa I-56127 Pisa Italy International Centre for Theoretical Sciences Tata Institute of Fundamental Research Bengaluru 560089 India Gravitational Wave Science Project National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan Advanced Technology Center National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan California State University Fullerton Fullerton California 92831 USA NCSA University of Illi

We report on an all-sky search for continuous gravitational waves in the frequency band 20–2000 Hz and with a frequency time derivative in the range of [−1.0,+0.1]×10−8 Hz/s. Such a signal could be produced by a nearby, spinning and slightly nonaxisymmetric isolated neutron star in our Galaxy. This search uses the LIGO data from the first six months of Advanced LIGO’s and Advanced Virgo’s third observational run, O3. No periodic gravitational wave signals are observed, and 95% confidence-level (C.L.) frequentist upper limits are placed on their strengths. The lowest upper limits on worst-case (linearly polarized) strain amplitude h0 are ∼1.7×10−25 near 200 Hz. For a circularly polarized source (most favorable orientation), the lowest upper limits are ∼6.3×10−26. These strict frequentist upper limits refer to all sky locations and the entire range of frequency derivative values. For a population-averaged ensemble of sky locations and stellar orientations, the lowest 95% C.L. upper limits on the strain amplitude are ∼1.4×10−25. These upper limits improve upon our previously published all-sky results, with the greatest improvement (factor of ∼2) seen at higher frequencies, in part because quantum squeezing has dramatically improved the detector noise level relative to the second observational run, O2. These limits are the most constraining to date over most of the parameter space searched.

关键词： Astrophysical studies of gravity Gravitational wave detection Gravitational wave sources Gravitational waves

Coherent spin control of s-, p-, d- and f-electrons in a silicon quantum dot

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arXiv 2019年

作者： Leon, R.C.C. Yang, C.H. Hwang, J.C.C. Lemyre, J. Camirand Tanttu, T. Huang, W. Chan, K.W. Tan, K.Y. Hudson, F.E. Itoh, K.M. Morello, A. Laucht, A. Pioro-Ladrière, M. Saraiva, A. Dzurak, A.S. Centre for Quantum Computation and Communication Technology School of Electrical Engineering and Telecommunications University of New South Wales SydneyNSW2052 Australia Institut Quantique et Département de Physique Université de Sherbrooke SherbrookeQCJ1K 2R1 Canada QCD Labs COMP Centre of Excellence Department of Applied Physics Aalto University Aalto00076 Finland School of Fundamental Science and Technology Keio University 3-14-1 Hiyoshi Kohokuku Yokohama223-8522 Japan Quantum Information Science Program Canadian Institute for Advanced Research TorontoONM5G 1Z8 Canada Research and Prototype Foundry University of Sydney SydneyNSW2006 Australia

Once the periodic properties of elements were unveiled, chemical bonds could be understood in terms of the valence of atoms. Ideally, this rationale would extend to quantum dots, often termed artificial atoms, and quantum computation could be performed by merely controlling the outer-shell electrons of dot-based qubits. Imperfections in the semiconductor material, including at the atomic scale, disrupt this analogy between atoms and quantum dots, so that real devices seldom display such a systematic many-electron arrangement. We demonstrate here an electrostaticallydefined quantum dot that is robust to disorder, revealing a well defined shell structure. We observe four shells (31 electrons) with multiplicities given by spin and valley degrees of freedom. We explore various fillings consisting of a single valence electron – namely 1, 5, 13 and 25 electrons – as potential qubits, and we identify fillings that yield a total spin-1 on the dot. An integrated micromagnet allows us to perform electrically-driven spin resonance (EDSR). Higher shell states are shown to be more susceptible to the driving field, leading to faster Rabi rotations of the qubit. We investigate the impact of orbital excitations of the p- and d-shell electrons on single qubits as a function of the dot deformation. This allows us to tune the dot excitation spectrum and exploit it for faster qubit control. Furthermore, hotspots arising from this tunable energy level structure provide a pathway towards fast spin initialisation. The observation of spin-1 states may be exploited in the future to study symmetry-protected topological states in antiferromagnetic spin chains and their application to quantum computing. Copyright © 2019, The Authors. All rights reserved.

关键词： Semiconductor quantum dots

Fermi level pinning by defects can explain the large reported carbon 1s binding energy variations in diamond

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arXiv 2019年

作者： Walter, Michael Mangolini, Filippo McClimon, J. Brandon Carpick, Robert W. Moseler, Michael Fraunhofer IWM MikroTribologie Centrum μTC Wöhlerstrasse 11 FreiburgD-79108 Germany FIT Freiburg Centre for Interactive Materials and Bioinspired Technologies University of Freiburg Georges-Köhler-Allee 105 Freiburg79110 Germany Institute of Physics University of Freiburg Herrmann-Herder-Straße 3 FreiburgD-79104 Germany Materials Science and Engineering Program Department of Mechanical Engineering University of Texas at Austin AustinTX78712 United States Department of Materials Science and Engineering University of Pennsylvania Philadelphia19104 United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania PhiladelphiaPA19104 United States Freiburger Materialforschungszentrum Universität Freiburg Stefan-Meier-Straße 21 FreiburgD-79104 Germany

The quantitative evaluation of the carbon hybridization state by X-ray photoelectron spectroscopy (XPS) has been a surface-analysis problem for the last three decades due to the challenges associated with the unambiguous identification of the characteristic binding energy values for sp2and sp3- bonded carbon. While the sp2binding energy is well established, there is disagreement for the sp3value in the literature. Here, we compute the binding energy values for model structures of pure and doped-diamond using density functional theory. The simulation results indicate that the large bandgap of diamond allows defects to pin the Fermi level, which results in large variations of the C(1s) core electron energies for sp3-bonded carbon, in agreement with the broad range of experimental C(1s) binding energy values for sp3. carbon reported in the literature. Fermi level pinning by boron is demonstrated by experimental C(1s) binding energies of highly B-doped ultrananocrystalline diamond that are in good agreement to simulations. Copyright © 2019, The Authors. All rights reserved.

关键词： Binding energy

Seasonal Variation of the Monthly Efficiencies of Thin Film PV Modules 5

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Seasonal Variation of the Monthly Efficiencies of Thin Film ...

5th International Renewable and Sustainable Energy Conference, IRSEC 2017

作者： Özden, Talat Turan, Raşit Akmoǧlu, Bülent Gültekin Department of Electrical and Electronics Engineering Gümüşhane University Günüşhane29100 Turkey Ankara06800 Turkey Department of Physics Faculty of Arts and Sciences METU Ankara06800 Turkey Earth System Science Program Graduate School of Natural and Applied Sciences METU Ankara06800 Turkey

ISBN: (纸本)9781538628478

Outdoor testing of solar photovoltaic (PV) modules must be carried out at different climates as PV power plants nowadays are installed and continues to be installed in many countries. Present study is outdoor testing results and analyses of 5 thin film modules in Ankara, Turkey. The analyses are carried out using monthly efficiencies of the modules that are derived using the energy yield and input. The average efficiencies of the CIS, CIGS and μc-Si/a-Si thin film modules are. We present the monthly and average efficiencies and discuss their variations with the parameter: input, ambient temperature and relative humidity. We also carried out seasonal analyses using Pearson's correlation coefficient and find out that the efficiencies are differently dependent on the above mentioned parameters. This arose a new open question on differentiation of the strength of the effect of each parameter on the monthly efficiencies. © 2017 IEEE.

关键词： Solar energy