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6th International Conference on Mathematical Aspects of Computer and Information Sciences, MACIS 2015

作者： Brake, Daniel A. Bates, Daniel J. Putkaradze, Vakhtang Maciejewski, Anthony A. Department of Applied and Computational Mathematics and Statistics University of Notre Dame Notre Dame United States Department of Mathematics Colorado State University Fort Collins United States Department of Mathematical and Statistical Sciences University of Alberta Edmonton Canada Department of Electrical and Computer Engineering Colorado State University Fort Collins United States

ISBN: (纸本)9783319328584

Cooperating robotic systems, especially in the context of fault-tolerance of complex robotic mechanisms, is an important question for theoretical and applied studies. In this paper, we focus on one measure of fault tolerance in robots, namely, the multiplicity of the configurations for reaching a particular point in the workspace, which is difficult to measure using traditional methods. As a particular example, we consider the case of a free-swinging failure of a robotic arm that is handled by having a cooperating functional robot grasp the link adjacent to the failed joint. We present an efficient method to compute the multiplicity measure of the workspace, based on the tools from numerical algebraic geometry, applied to the inverse kinematics problem re-cast in the form of a polynomial system. To emphasize the difference between our methods and more traditional approaches, we compute the measure of workspace based on the multiplicity of configurations, and optimize placement of synergistic robot arms and the optimal grasp point on each link of the broken robot based on this measure. © Springer International Publishing Switzerland 2016.

关键词： Fault tolerance

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Hyperuniformity and its generalizations

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Physical Review E 2016年第2期94卷 022122-022122页

作者： Salvatore Torquato Department of Chemistry Department of Physics Princeton Center for Theoretical Science Program of Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystal and liquid: They are like perfect crystals in the way they suppress large-scale density fluctuations and yet are like liquids or glasses in that they are statistically isotropic with no Bragg peaks. These exotic states of matter play a vital role in a number of problems across the physical, mathematical as well as biological sciences and, because they are endowed with novel physical properties, have technological importance. Given the fundamental as well as practical importance of disordered hyperuniform systems elucidated thus far, it is natural to explore the generalizations of the hyperuniformity notion and its consequences. In this paper, we substantially broaden the hyperuniformity concept along four different directions. This includes generalizations to treat fluctuations in the interfacial area (one of the Minkowski functionals) in heterogeneous media and surface-area driven evolving microstructures, random scalar fields, divergence-free random vector fields, and statistically anisotropic many-particle systems and two-phase media. In all cases, the relevant mathematical underpinnings are formulated and illustrative calculations are provided. Interfacial-area fluctuations play a major role in characterizing the microstructure of two-phase systems (e.g., fluid-saturated porous media), physical properties that intimately depend on the geometry of the interface, and evolving two-phase microstructures that depend on interfacial energies (e.g., spinodal decomposition). In the instances of random vector fields and statistically anisotropic structures, we show that the standard definition of hyperuniformity must be generalized such that it accounts for the dependence of the relevant spectral functions on the direction in which the origin in Fourier space is approached (nonanalyticities at the origin). Using this analysis, we place some well-known energy spectr

关键词： Amorphous materials Glasses

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Critical slowing down and hyperuniformity on approach to jamming

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Physical Review E 2016年第1期94卷 012902-012902页

作者： Steven Atkinson Ge Zhang Adam B. Hopkins Salvatore Torquato Department of Chemistry Department of Physics Princeton Center for Theoretical Science Program of Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

Hyperuniformity characterizes a state of matter that is poised at a critical point at which density or volume-fraction fluctuations are anomalously suppressed at infinite wavelengths. Recently, much attention has been given to the link between strict jamming (mechanical rigidity) and (effective or exact) hyperuniformity in frictionless hard-particle packings. However, in doing so, one must necessarily study very large packings in order to access the long-ranged behavior and to ensure that the packings are truly jammed. We modify the rigorous linear programming method of Donev et al. [J. Comput. Phys. 197, 139 (2004)] in order to test for jamming in putatively collectively and strictly jammed packings of hard disks in two dimensions. We show that this rigorous jamming test is superior to standard ways to ascertain jamming, including the so-called “pressure-leak” test. We find that various standard packing protocols struggle to reliably create packings that are jammed for even modest system sizes of N≈103 bidisperse disks in two dimensions; importantly, these packings have a high reduced pressure that persists over extended amounts of time, meaning that they appear to be jammed by conventional tests, though rigorous jamming tests reveal that they are not. We present evidence that suggests that deviations from hyperuniformity in putative maximally random jammed (MRJ) packings can in part be explained by a shortcoming of the numerical protocols to generate exactly jammed configurations as a result of a type of “critical slowing down” as the packing's collective rearrangements in configuration space become locally confined by high-dimensional “bottlenecks” from which escape is a rare event. Additionally, various protocols are able to produce packings exhibiting hyperuniformity to different extents, but this is because certain protocols are better able to approach exactly jammed configurations. Nonetheless, while one should not generally expect exact hyperuniformity for d

关键词： Granular materials Packing & jamming problems

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Static structural signatures of nearly jammed disordered and ordered hard-sphere packings: Direct correlation function

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Physical Review E 2016年第3期94卷 032902-032902页

作者： Steven Atkinson Frank H. Stillinger Salvatore Torquato Department of Chemistry Department of Physics Princeton Center for Theoretical Science Program of Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

The nonequilibrium process by which hard-particle systems may be compressed into disordered, jammed states has received much attention because of its wide utility in describing a broad class of amorphous materials. While dynamical signatures are known to precede jamming, the task of identifying static structural signatures indicating the onset of jamming have proven more elusive. The observation that compressing hard-particle packings towards jamming is accompanied by an anomalous suppression of density fluctuations (termed “hyperuniformity”) has paved the way for the analysis of jamming as an “inverted critical point” in which the direct correlation function c(r), rather than the total correlation function h(r), diverges. We expand on the notion that c(r) provides both universal and protocol-specific information as packings approach jamming. By considering the degree and position of singularities (discontinuities in the nth derivative) as well as how they are changed by the convolutions found in the Ornstein-Zernike equation, we establish quantitative statements about the structure of c(r) with regards to singularities it inherits from h(r). These relations provide a concrete means of identifying features that must be expressed in c(r) if one hopes to reproduce various details in the pair correlation function accurately and provide stringent tests on the associated numerics. We also analyze the evolution of systems of three-dimensional monodisperse hard spheres of diameter D as they approach ordered and disordered jammed configurations. For the latter, we use the Lubachevsky-Stillinger (LS) molecular dynamics and Torquato-Jiao (TJ) sequential linear programming algorithms, which both generate disordered packings, but can show perceptible structural differences. We identify a short-ranged scaling c(r)∝−1/r as r→0 that accompanies the formation of the delta function at c(D) that indicates the formation of contacts in all cases, and show that this scaling behavior is,

关键词： Jamming

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Multimuons in cosmic-ray events as seen in ALICE at the LHC

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Journal of Cosmology and Astroparticle Physics 2025年第4期2025卷 009-009页

作者： Acharya, S. Agarwal, A. Aglieri Rinella, G. Aglietta, L. Agnello, M. Agrawal, N. Ahammed, Z. Ahmad, S. Ahn, S.U. Ahuja, I. Akindinov, A. Akishina, V. Al-Turany, M. Aleksandrov, D. Alessandro, B. Alfanda, H.M. Alfaro Molina, R. Ali, B. Alici, A. Alizadehvandchali, N. Alkin, A. Alme, J. Alocco, G. Alt, T. Altamura, A.R. Altsybeev, I. Alvarado, J.R. Alvarez, C.O.R. Anaam, M.N. Andrei, C. Andreou, N. Andronic, A. Andronov, E. Anguelov, V. Antinori, F. Antonioli, P. Apadula, N. Aphecetche, L. Appelshäuser, H. Arata, C. Arcelli, S. Arnaldi, R. Arneiro, J.G.M.C.A. Arsene, I.C. Arslandok, M. Augustinus, A. Averbeck, R. Averyanov, D. Azmi, M.D. Baba, H. Badalà, A. Bae, J. Bae, Y. Baek, Y.W. Bai, X. Bailhache, R. Bailung, Y. Bala, R. Balbino, A. Baldisseri, A. Balis, B. Banoo, Z. Barbasova, V. Barile, F. Barioglio, L. Barlou, M. Barman, B. Barnaföldi, G.G. Barnby, L.S. Barreau, E. Barret, V. Barreto, L. Bartels, C. Barth, K. Bartsch, E. Bastid, N. Basu, S. Batigne, G. Battistini, D. Batyunya, B. Bauri, D. Bazo Alba, J.L. Bearden, I.G. Beattie, C. Becht, P. Behera, D. Belikov, I. Bell Hechavarria, A.D.C. Bellini, F. Bellwied, R. Belokurova, S. Beltran, L.G.E. Beltran, Y.A.V. Bencedi, G. Bensaoula, A. Beole, S. Berdnikov, Y. Berdnikova, A. Bergmann, L. Besoiu, M.G. Betev, L. Bhaduri, P.P. Bhasin, A. Bhattacharjee, B. Bianchi, L. Bielčík, J. Bielčíková, J. Bigot, A.P. Bilandzic, A. Biro, G. Biswas, S. Bize, N. Blair, J.T. Blau, D. Blidaru, M.B. Bluhme, N. Blume, C. Bock, F. Bodova, T. Bok, J. Boldizsár, L. Bombara, M. Bond, P.M. Bonomi, G. Borel, H. Borissov, A. Borquez Carcamo, A.G. Botta, E. Bouziani, Y.E.M. Bratrud, L. Braun-Munzinger, P. Bregant, M. Broz, M. Bruno, G.E. Buchakchiev, V.D. Buckland, M.D. Budnikov, D. Buesching, H. Bufalino, S. Buhler, P. Burmasov, N. Buthelezi, Z. Bylinkin, A. Bysiak, S.A. Cabanillas Noris, J.C. Cabrera, M.F.T. Caines, H. Caliva, A. Calvo Villar, E. Camacho, J.M.M. Camerini, P. Canedo, F.D.M. Cantway, S.L. Carabas, M. Carballo, A.A. Carnesecchi, F. Caron, R. Carvalho, L.A.D. Castillo Castel A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute) Foundation Yerevan Armenia AGH University of Krakow Cracow Poland Bogolyubov Institute for Theoretical Physics National Academy of Sciences of Ukraine Kiev Ukraine Bose Institute Department of Physics Centre for Astroparticle Physics and Space Science (CAPSS) Kolkata India California Polytechnic State University San Luis Obispo CA United States Central China Normal University Wuhan China Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear (CEADEN) Havana Cuba Centro de Investigación y de Estudios Avanzados (CINVESTAV) Mérida Mexico City Mexico Chicago State University Chicago IL United States China Institute of Atomic Energy Beijing China China University of Geosciences Wuhan China Chungbuk National University Cheongju South Korea Comenius University Bratislava Faculty of Mathematics Physics and Informatics Bratislava Slovakia Creighton University Omaha NE United States Department of Physics Aligarh Muslim University Aligarh India Department of Physics Pusan National University Pusan South Korea Department of Physics Sejong University Seoul South Korea Department of Physics University of California Berkeley CA United States Department of Physics University of Oslo Oslo Norway Department of Physics and Technology University of Bergen Bergen Norway Dipartimento di Fisica Università di Pavia Pavia Italy Dipartimento di Fisica dell’Università Sezione INFN Cagliari Italy Dipartimento di Fisica dell’Università Sezione INFN Trieste Italy Dipartimento di Fisica dell’Università Sezione INFN Turin Italy Dipartimento di Fisica e Astronomia dell’Università Sezione INFN Bologna Italy Dipartimento di Fisica e Astronomia dell’Università Sezione INFN Catania Italy Dipartimento di Fisica e Astronomia dell’Università Sezione INFN Padova Italy Dipartimento di Fisica ‘E.R. Caianiello’ dell’Università Gruppo Collegato INFN Salerno Italy Dipartimento DISAT del Politecnico Sezione

ALICE is a large experiment at the CERN Large Hadron Collider. Located 52 meters underground, its detectors are suitable to measure muons produced by cosmic-ray interactions in the atmosphere. In this paper, the studies of the cosmic muons registered by ALICE during Run 2 (2015–2018) are described. The analysis is limited to multimuon events defined as events with more than four detected muons (N_µ > 4) and in the zenith angle range 0^◦ < θ < 50^◦. The results are compared with Monte Carlo simulations using three of the main hadronic interaction models describing the air shower development in the atmosphere: QGSJET-II-04, EPOS-LHC, and SIBYLL 2.3d. The interval of the primary cosmic-ray energy involved in the measured muon multiplicity distribution is about 4×10¹⁵ < E_prim < 6×10¹⁶ eV. In this interval none of the three models is able to describe precisely the trend of the composition of cosmic rays as the energy increases. However, QGSJET-II-04 is found to be the only model capable of reproducing reasonably well the muon multiplicity distribution, assuming a heavy composition of the primary cosmic rays over the whole energy range, while SIBYLL 2.3d and EPOS-LHC underpredict the number of muons in a large interval of multiplicity by more than 20% and 30%, respectively. The rate of high muon multiplicity events (N_µ > 100) obtained with QGSJET-II-04 and SIBYLL 2.3d is compatible with the data, while EPOS-LHC produces a significantly lower rate (55% of the measured rate). For both QGSJET-II-04 and SIBYLL 2.3d, the rate is close to the data when the composition is assumed to be dominated by heavy elements, an outcome compatible with the average energy E_prim ∼ 10¹⁷ eV of these events. This result places significant constraints on more exotic production mechanisms. © 2025 The Author(s).

关键词： cosmic ray experiments cosmic rays detectors

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A multi-scale Gaussian beam parametrix for the wave equation: The Dirichlet boundary value problem.

arXiv

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arXiv 2017年

作者： Berra, Michele de Hoop, Maarten V. Romero, José Luis corso Duca degli Abruzzi 24 Torino10129 Italy Department of Computational and Applied Mathematics Rice University 6100 Main MS-134 HoustonTX77005 United States Acoustics Research Institute Austrian Academy of Sciences Wohllebengasse 12-14 Vienna1040 Austria

We present a construction of a multi-scale Gaussian beam parametrix for the Dirichlet boundary value problem associated with the wave equation, and study its convergence rate to the true solution in the highly oscillatory regime. The construction elaborates on the wave-atom parametrix of Bao, Qian, Ying, and Zhang and extends to a multi-scale setting the technique of Gaussian beam propagation from a boundary of Katchalov, Kurylev and Lassas.35L05, 35L20, 35S05, 42C15.35L05, 35L20, 35S05, 42C15 Copyright © 2017, The Authors. All rights reserved.

关键词： Gaussian beams

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Basic results on Crisp boolean petri nets 1

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1st International Conference on Modern Mathematical Methods and High Performance Computing in Science and Technology, M3HPCST 2015

作者： Singh, Gajendra Pratap Kansal, Sangita School of Computational and Integrative Sciences Jawaharlal Nehru University New Mehrauli Road New Delhi110067 India Department of Applied Mathematics Delhi Technological University New Delhi110042 India

ISBN: (数字)9789811014543

ISBN: (纸本)9789811014536

The concept of Petri net as a discrete event-driven dynamical system was invented by Carl Adam Petri in his doctoral thesis ‘Communication with Automata’ in 1962. Petri nets are one of the best defined approach to modeling of discrete and concurrent systems. The dynamics of Petri nets represent the long-term behavior of the modeled system. Petri nets combine mathematical concepts with a pictorial representation of the dynamical behavior of the modeled systems. A Petri net is a bipartite directed graph consisting of two type of nodes, namely, place nodes and transition nodes. Directed arcs connect places to transitions and transitions to places to represent flow relation. In this paper, we present some basic results on 1-safe Petri net that generates every binary n-vector exactly once as marking vectors in its reachability tree, known as crisp Boolean Petri net. These results can be used for characterizing crisp Boolean Petri nets. © Springer Science+Business Media Singapore 2016.

关键词： Petri nets

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Proton emission in ultraperipheral Pb-Pb collisions at sNN=5.02 TeV

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Physical Review C 2025年第5期111卷 054906-054906页

作者： S. Acharya A. Agarwal G. Aglieri Rinella L. Aglietta M. Agnello N. Agrawal Z. Ahammed S. Ahmad S. U. Ahn I. Ahuja A. Akindinov V. Akishina M. Al-Turany D. Aleksandrov B. Alessandro H. M. Alfanda R. Alfaro Molina B. Ali A. Alici N. Alizadehvandchali A. Alkin J. Alme G. Alocco T. Alt A. R. Altamura I. Altsybeev J. R. Alvarado C. O. R. Alvarez M. N. Anaam C. Andrei N. Andreou A. Andronic E. Andronov V. Anguelov F. Antinori P. Antonioli N. Apadula L. Aphecetche H. Appelshäuser C. Arata S. Arcelli R. Arnaldi J. G. M. C. A. Arneiro I. C. Arsene M. Arslandok A. Augustinus R. Averbeck D. Averyanov M. D. Azmi H. Baba A. Badalà J. Bae Y. Bae Y. W. Baek X. Bai R. Bailhache Y. Bailung R. Bala A. Baldisseri B. Balis Z. Banoo V. Barbasova F. Barile L. Barioglio M. Barlou B. Barman G. G. Barnaföldi L. S. Barnby E. Barreau V. Barret L. Barreto C. Bartels K. Barth E. Bartsch N. Bastid S. Basu G. Batigne D. Battistini B. Batyunya D. Bauri J. L. Bazo Alba I. G. Bearden C. Beattie P. Becht D. Behera I. Belikov A. D. C. Bell Hechavarria F. Bellini R. Bellwied S. Belokurova L. G. E. Beltran Y. A. V. Beltran G. Bencedi A. Bensaoula S. Beole Y. Berdnikov A. Berdnikova L. Bergmann M. G. Besoiu L. Betev P. P. Bhaduri A. Bhasin B. Bhattacharjee L. Bianchi J. Bielčík J. Bielčíková A. P. Bigot A. Bilandzic A. Binoy G. Biro S. Biswas N. Bize J. T. Blair D. Blau M. B. Blidaru N. Bluhme C. Blume F. Bock T. Bodova J. Bok L. Boldizsár M. Bombara P. M. Bond G. Bonomi H. Borel A. Borissov A. G. Borquez Carcamo E. Botta Y. E. M. Bouziani D. C. Brandibur L. Bratrud P. Braun-Munzinger M. Bregant M. Broz G. E. Bruno V. D. Buchakchiev M. D. Buckland D. Budnikov H. Buesching S. Bufalino P. Buhler N. Burmasov Z. Buthelezi A. Bylinkin S. A. Bysiak J. C. Cabanillas Noris M. F. T. Cabrera H. Caines A. Caliva E. Calvo Villar J. M. M. Camacho P. Camerini F. D. M. Canedo S. L. Cantway M. Carabas A. A. Carballo F. Carnesecchi R. Caron L. A. D. Carvalho J. Castillo Castellanos M. Castoldi F. Catalano S. Cattaruzzi R. Cerri I. Chakaberia P. Chakraborty S. Chandra Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Variable Energy Cyclotron Centre Homi Bhabha National Institute Kolkata India European Organization for Nuclear Research (CERN) Geneva Switzerland Dipartimento di Fisica dell'Università and Sezione INFN Turin Italy Dipartimento DISAT del Politecnico and Sezione INFN Turin Italy Dipartimento di Fisica e Astronomia dell'Università and Sezione INFN Bologna Italy Department of Physics Aligarh Muslim University Aligarh India Korea Institute of Science and Technology Information Daejeon Republic of Korea Faculty of Science P.J. Šafárik University Košice Slovak Republic Affiliated with an institute covered by a cooperation agreement with CERN Frankfurt Institute for Advanced Studies Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany Research Division and ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Darmstadt Germany INFN Sezione di Torino Turin Italy Central China Normal University Wuhan China Instituto de Física Universidad Nacional Autónoma de México Mexico City Mexico University of Houston Houston Texas USA Sungkyunkwan University Suwon City Republic of Korea Department of Physics and Technology University of Bergen Bergen Norway INFN Sezione di Cagliari Cagliari Italy Institut für Kernphysik Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany INFN Sezione di Bari Bari Italy Physik Department Technische Universität München Munich Germany High Energy Physics Group Universidad Autónoma de Puebla Puebla Mexico Horia Hulubei National Institute of Physics and Nuclear Engineering Bucharest Romania University of Derby Derby United Kingdom Universität Münster Institut für Kernphysik Münster Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany INFN Sezione di Padova Padova Italy INFN Sezione di Bologna Bologna Italy Lawrence Berkeley National Laboratory Berkeley California USA SUBATECH I

The first measurements of proton emission accompanied by neutron emission in the electromagnetic dissociation (EMD) of Pb208 nuclei in the ALICE experiment at the Large Hadron Collider are presented. The EMD protons and neutrons emitted at very forward rapidities are detected by the proton and neutron zero degree calorimeters of the ALICE experiment. The emission cross sections of zero, one, two, and three protons accompanied by at least one neutron were measured in ultraperipheral Pb208−Pb208 collisions at a center-of-mass energy per nucleon pair sNN=5.02TeV. The 0p and 3p cross sections are described by the RELDIS model within their measurement uncertainties, while the 1p and 2p cross sections are underestimated by the model by 17–25%. According to this model, these 0p, 1p, 2p, and 3p cross sections are associated, respectively, with the production of various isotopes of Pb, Tl, Hg, and Au in the EMD of Pb208. The cross sections of the emission of a single proton accompanied by the emission of one, two, or three neutrons in EMD were also measured. The data are significantly overestimated by the RELDIS model, which predicts that the (1p,1n), (1p,2n), and (1p,3n) cross sections are very similar to the cross sections for the production of the thallium isotopes Tl206,205,204.

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Probability current in zero-spin relativistic quantum mechanics

arXiv

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arXiv 2017年

作者： Fülöp, Tamás Matolcsi, Tamás Department of Energy Engineering Budapest University of Technology and Economics 3 Műegyetem rkp. Budapest1111 Hungary Department of Applied Analysis and Computational Mathematics Eötvös Loránd University 1/C Pázmány P. Stny. Budapest1117 Hungary

We show that the antisymmetric spinor tensor representation of spin-0 relativistic quantum mechanics provides a conserved current with positive definite timelike component, interpretable as probability density. The construction runs in complete analogy to the spin-1/2 case, and provides an analogously natural one-particle Hilbert space description for spin 0. Except for the free particle, the obtained formulation proves to be inequivalent to the one based on the Klein-Gordon equation. The second quantized version may lead to new field theoretical interaction terms for zero-spin particles.1. Copyright © 2017, The Authors. All rights reserved.

关键词： Equations of motion

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Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L (vol 50, pg 1565, 2018)

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NATURE GENETICS 2018年第12期50卷 1754-1754页

作者： Zhang, Jisen Zhang, Xingtan Tang, Haibao Zhang, Qing Hua, Xiuting Ma, Xiaokai Zhu, Fan Jones, Tyler Zhu, Xinguang Bowers, John Wai, Ching Man Zheng, Chunfang Shi, Yan Chen, Shuai Xu, Xiuming Yue, Jingjing Nelson, David R. Huang, Lixian Li, Zhen Xu, Huimin Zhou, Dong Wang, Yongjun Hu, Weichang Lin, Jishan Deng, Youjin Pandey, Neha Mancini, Melina Zerpa, Dessiree Nguyen, Julie K. Wang, Liming Yu, Liang Xin, Yinghui Ge, Liangfa Arro, Jie Han, Jennifer O. Chakrabarty, Setu Pushko, Marija Zhang, Wenping Ma, Yanhong Ma, Panpan Lv, Mingju Chen, Faming Zheng, Guangyong Xu, Jingsheng Yang, Zhenhui Deng, Fang Chen, Xuequn Liao, Zhenyang Zhang, Xunxiao Lin, Zhicong Lin, Hai Yan, Hansong Kuang, Zheng Zhong, Weimin Liang, Pingping Wang, Guofeng Yuan, Yuan Shi, Jiaxian Hou, Jinxiang Lin, Jingxian Jin, Jingjing Cao, Peijian Shen, Qiaochu Jiang, Qing Zhou, Ping Ma, Yaying Zhang, Xiaodan Xu, Rongrong Liu, Juan Zhou, Yongmei Jia, Haifeng Ma, Qing Qi, Rui Zhang, Zhiliang Fang, Jingping Fang, Hongkun Song, Jinjin Wang, Mengjuan Dong, Guangrui Wang, Gang Chen, Zheng Ma, Teng Liu, Hong Dhungana, Singha R. Huss, Sarah E. Yang, Xiping Sharma, Anupma Trujillo, Jhon H. Martinez, Maria C. Hudson, Matthew Riascos, John J. Schuler, Mary Chen, Li-Qing Braun, David M. Li, Lei Yu, Qingyi Wang, Jianping Wang, Kai Schatz, Michael C. Heckerman, David Van Sluys, Marie-Anne Souza, Glaucia Mendes Moore, Paul H. Sankoff, David VanBuren, Robert Paterson, Andrew H. Nagai, Chifumi Ming, Ray Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology National Sugarcane Engineering Technology Research Center Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou China Department of Plant Biology University of Illinois at Urbana-Champaign Urbana IL USA Hawaii Agriculture Research Center Kunia HI USA Institute for Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China Department of Plant Biology University of Georgia Athens GA USA Department of Horticulture Michigan State University East Lansing MI USA Department of Mathematics and Statistics University of Ottawa Ottawa Ontario Canada Department of Microbiology Immunology and Biochemistry University of Tennessee HSC Memphis TN USA Chinese Academy of Sciences-Max-Planck-Gesellschaft Partner Institute for Computational Biology Chinese Academy of Sciences Shanghai China China Tobacco Gene Research Center Zhengzhou Tobacco Research Institute of CNTC Zhengzhou China Division of Biological Sciences University of Missouri Columbia MO USA Department of Agronomy University of Florida Gainesville FL USA Texas A&M AgriLife Research Texas A&M University System Dallas TX USA Centro de Investigación de la Caña de Azúcar de Colombia (Cenicaña) Cali Colombia Department of Crop Sciences University of Illinois at Urbana-Champaign Urbana IL USA Departments of Computer Science and Biology Johns Hopkins University Baltimore MD USA Microsoft Research Redmond WA USA Departamento de Botânica Instituto de Biociências Universidade de São Paulo São Paulo Brazil Departamento de Bioquímica Instituto de Química Universidade de São Paulo São Paulo Brazil

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

关键词： Genomics Plant genetics

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