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  • 1
    Publication Date: 2016-05-17
    Description: Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent—due to events such as incomplete lineage sorting or horizontal gene transfer—it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward’s method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta . We release treeCl, a new program to cluster genes of common evolutionary history ( http://git.io/treeCl ).
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 2
    Publication Date: 2015-03-27
    Description: Author(s): N. Goldman, J. Dalibard, M. Aidelsburger, and N. R. Cooper Quantum systems can show qualitatively new forms of behavior when they are driven by fast time-periodic modulations. In the limit of large driving frequency, the long-time dynamics of such systems can often be described by a time-independent effective Hamiltonian, which is generally identified throu... [Phys. Rev. A 91, 033632] Published Thu Mar 26, 2015
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 3
    Publication Date: 2016-07-01
    Description: Nature Physics 12, 639 (2016). doi:10.1038/nphys3803 Authors: N. Goldman, J. C. Budich & P. Zoller
    Print ISSN: 1745-2473
    Electronic ISSN: 1745-2481
    Topics: Physics
    Published by Springer Nature
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  • 4
    Publication Date: 2016-06-08
    Description: Author(s): H. M. Price, O. Zilberberg, T. Ozawa, I. Carusotto, and N. Goldman The remarkable quantization of the Hall conductivity is routinely observed in two-dimensional electron gases subject to strong magnetic fields. Such quantum transport experiments are performed by measuring the current that flows in 2D systems in response to an applied electric field, and result in a quantized conductance proportional to a topological index, known as the Chern number. Recently, a similar effect was proposed and observed in gases of ultracold atoms, when these are loaded into Bloch bands with a nonzero Chern number. In this context, the center of mass of the atomic gas performs a measurable differential drift, in direct analogy with the electronic Hall effect, from which the corresponding Chern number can be obtained. Such detection relies on the assumption that the center-of-mass drift of the atomic cloud is directly related to the current density, which itself depends on the Chern number of the band. Here, the authors carefully revisit and analyze the center-of-mass detection scheme. Interestingly, we find that the center-of-mass motion also depends on the particle density, which in the presence of magnetic perturbations, can be explicitly related to the topology of the band. Whereas this additional dependence offers a correction to existing experimental results, it opens up a rich variety of new possible quantized responses and detection schemes in 2D and 4D engineered systems, such as cold atoms and photonic lattices. [Phys. Rev. B 93, 245113] Published Mon Jun 06, 2016
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 5
    Publication Date: 2015-06-25
    Description: Author(s): N. Goldman and J. Dalibard [Phys. Rev. X 5, 029902] Published Mon Jun 22, 2015
    Electronic ISSN: 2160-3308
    Topics: Physics
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  • 6
    Publication Date: 2015-02-04
    Description: Nature Physics 11, 162 (2015). doi:10.1038/nphys3171 Authors: M. Aidelsburger, M. Lohse, C. Schweizer, M. Atala, J. T. Barreiro, S. Nascimbène, N. R. Cooper, I. Bloch & N. Goldman Sixty years ago, Karplus and Luttinger pointed out that quantum particles moving on a lattice could acquire an anomalous transverse velocity in response to a force, providing an explanation for the unusual Hall effect in ferromagnetic metals. A striking manifestation of this transverse transport was then revealed in the quantum Hall effect where the plateaux depicted by the Hall conductivity were attributed to a topological invariant characterizing the Bloch bands: the Chern number. Until now, topological transport associated with non-zero Chern numbers has only been observed in electronic systems. Here we use the transverse deflection of an atomic cloud in response to an optical gradient to measure the Chern number of artificially generated Hofstadter bands. These topological bands are very flat and thus constitute good candidates for the realization of fractional Chern insulators. Combining these deflection measurements with the determination of the band populations, we obtain an experimental value for the Chern number of the lowest band νexp = 0.99(5). This first Chern-number measurement in a non-electronic system is facilitated by an all-optical artificial gauge field scheme, generating uniform flux in optical superlattices.
    Print ISSN: 1745-2473
    Electronic ISSN: 1745-2481
    Topics: Physics
    Published by Springer Nature
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  • 7
    Publication Date: 2011-02-16
    Description: Author(s): D. Bercioux, N. Goldman, and D. F. Urban Physical phenomena driven by topological properties, such as the quantum Hall effect, have the appealing feature that they are robust with respect to external perturbations. Lately, a new class of materials has emerged that manifests topological properties at room temperature and without the need of... [Phys. Rev. A 83, 023609] Published Tue Feb 15, 2011
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 8
    Publication Date: 2011-06-03
    Description: Author(s): N. Goldman, D. F. Urban, and D. Bercioux We investigate the properties of the Lieb lattice, that is, a face-centered square lattice, subjected to external gauge fields. We show that an Abelian gauge field leads to a peculiar quantum Hall effect, which is a consequence of the single Dirac cone and the flat band characterizing the energy spe... [Phys. Rev. A 83, 063601] Published Thu Jun 02, 2011
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 9
    Publication Date: 2012-01-28
    Description: Author(s): Feng Mei, Shi-Liang Zhu, Zhi-Ming Zhang, C. H. Oh, and N. Goldman We propose an experimental scheme to simulate and detect the properties of time-reversal invariant topological insulators, using cold atoms trapped in one-dimensional bichromatic optical lattices. This system is described by a one-dimensional Aubry-Andre model with an additional SU(2) gauge structur... [Phys. Rev. A 85, 013638] Published Fri Jan 27, 2012
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 10
    Publication Date: 2014-08-19
    Description: Author(s): N. Goldman and J. Dalibard Topological effects can result from a material’s intrinsic properties, or can be generated by external electromagnetic fields or mechanical deformations. Researchers analyze how driven quantum systems can lead to new topological states of matter. [Phys. Rev. X 4, 031027] Published Mon Aug 18, 2014
    Electronic ISSN: 2160-3308
    Topics: Physics
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