@inproceedings{1042, abstract = {Recent years have seen tremendous progress in the field of cold and ultracold molecules. A central goal in the field is currently the realization of stable rovibronic ground-state molecular samples in the regime of quantum degeneracy, e.g. in the form of molecular Bose-Einstein condensates, molecular degenerate Fermi gases, or, when an optical lattice is present, molecular Mott-insulator phases. However, molecular samples are not readily cooled to the extremely low temperatures at which quantum degeneracy occurs. In particular, laser cooling, the \'workhorse\' for the field of atomic quantum gases, is generally not applicable to molecular samples. Here we take an important step beyond previous work1 and provide details on the realization of an ultracold quantum gas of ground-state dimer molecules trapped in an optical lattice as recently reported in Ref. 2. We demonstrate full control over all internal and external quantum degrees of freedom for the ground-state molecules by deterministically preparing the molecules in a single quantum state, i.e. in a specific hyperfine sublevel of the rovibronic ground state, while the molecules are trapped in the motional ground state of the individual lattice wells. We circumvent the problem of cooling by associating weakly-bound molecules out of a zero-temperature atomic Mott-insulator state and by transferring these to the absolute ground state in a four-photon STIRAP process. Our preparation procedure directly leads to a long-lived, lattice-trapped molecular many-body state, which we expect to form the platform for many of the envisioned future experiments with molecular quantum gases, e.g. on precision molecular spectroscopy, quantum information science, and dipolar quantum systems.}, author = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Hart, Russell and Nägerl, Hanns}, pages = {256 -- 269}, publisher = {World Scientific Publishing}, title = {{Production of a quantum gas of rovibronic ground-state molecules in an optical lattice}}, doi = {10.1142/9789814282345_0024}, year = {2010}, } @article{1044, abstract = {Control over all internal and external degrees of freedom of molecules at the level of single quantum states will enable a series of fundamental studies in physics and chemistry1,2. In particular, samples of ground-state molecules at ultralow temperatures and high number densities will facilitate new quantum-gas studies3 and future applications in quantum information science4. However, high phase-space densities for molecular samples are not readily attainable because efficient cooling techniques such as laser cooling are lacking. Here we produce an ultracold and dense sample of molecules in a single hyperfine level of the rovibronic ground state with each molecule individually trapped in the motional ground state of an optical lattice well. Starting from a zero-temperature atomic Mott-insulator state with optimized double-site occupancy6, weakly bound dimer molecules are efficiently associated on a Feshbach resonance7 and subsequently transferred to the rovibronic ground state by a stimulated four-photon process with >50% efficiency. The molecules are trapped in the lattice and have a lifetime of 8 s. Our results present a crucial step towards Bose-Einstein condensation of ground-state molecules and, when suitably generalized to polar heteronuclear molecules, the realization of dipolar quantum-gas phases in optical lattices8-10.}, author = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Hart, Russell and Aldegunde, Jesus and Hutson, Jeremy and Nägerl, Hanns}, journal = {Nature Physics}, number = {4}, pages = {265 -- 270}, publisher = {Nature Publishing Group}, title = {{An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice}}, doi = {10.1038/nphys1533}, volume = {6}, year = {2010}, } @article{1045, abstract = {We report on the observation of confinement-induced resonances in strongly interacting quantum-gas systems with tunable interactions for one- and two-dimensional geometry. Atom-atom scattering is substantially modified when the s-wave scattering length approaches the length scale associated with the tight transversal confinement, leading to characteristic loss and heating signatures. Upon introducing an anisotropy for the transversal confinement we observe a splitting of the confinement-induced resonance. With increasing anisotropy additional resonances appear. In the limit of a two-dimensional system we find that one resonance persists.}, author = {Haller, Elmar and Mark, Manfred and Hart, Russell and Danzl, Johann G and Reichsöllner, Lukas and Melezhik, Vladimir and Schmelcher, Peter and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {15}, publisher = {American Physical Society}, title = {{Confinement-induced resonances in low-dimensional quantum systems}}, doi = {10.1103/PhysRevLett.104.153203}, volume = {104}, year = {2010}, } @article{1046, abstract = {The phenomenon of matter-wave interference lies at the heart of quantum physics. It has been observed in various contexts in the limit of non-interacting particles as a single-particle effect. Here we observe and control matter-wave interference whose evolution is driven by interparticle interactions. In a multi-path matter-wave interferometer, the macroscopic manybody wave function of an interacting atomic Bose-Einstein condensate develops a regular interference pattern, allowing us to detect and directly visualize the effect of interaction-induced phase shifts. We demonstrate control over the phase evolution by inhibiting interaction-induced dephasing and by refocusing a dephased macroscopic matter wave in a spin-echo-type experiment. Our results show that interactions in a many-body system lead to a surprisingly coherent evolution, possibly enabling narrow-band and high-brightness matterwave interferometers based on atom lasers.}, author = {Gustavsson, Mattias and Haller, Elmar and Mark, Manfred and Danzl, Johann G and Hart, Russell and Daley, Andrew and Nägerl, Hanns}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Interference of interacting matter waves}}, doi = {10.1088/1367-2630/12/6/065029}, volume = {12}, year = {2010}, } @article{1047, abstract = {Particles in a perfect lattice potential perform Bloch oscillations when subject to a constant force, leading to localization and preventing conductivity. For a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass oscillations in position space with a displacement across hundreds of lattice sites when we add a periodic modulation to the force near the Bloch frequency. We study the dependence of these "super" Bloch oscillations on lattice depth, modulation amplitude, and modulation frequency and show that they provide a means to induce linear transport in a dissipation-free lattice.}, author = {Haller, Elmar and Hart, Russell and Mark, Manfred and Danzl, Johann G and Reichsöllner, Lukas and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Inducing transport in a dissipation-free lattice with super bloch oscillations}}, doi = {10.1103/PhysRevLett.104.200403}, volume = {104}, year = {2010}, } @article{1049, abstract = {Quantum many-body systems can have phase transitions even at zero temperature; fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to thermal effects, drive the system from one phase to another. Typically, during the transition the relative strength of two competing terms in the systemĝ€™s Hamiltonian changes across a finite critical value. A well-known example is the Mottĝ€" Hubbard quantum phase transition from a superfluid to an insulating phase, which has been observed for weakly interacting bosonic atomic gases. However, for strongly interacting quantum systems confined to lower-dimensional geometry, a novel type of quantum phase transition may be induced and driven by an arbitrarily weak perturbation to the Hamiltonian. Here we observe such an effectĝ€"the sineĝ€"Gordon quantum phase transition from a superfluid Luttinger liquid to a Mott insulatorĝ€ "in a one-dimensional quantum gas of bosonic caesium atoms with tunable interactions. For sufficiently strong interactions, the transition is induced by adding an arbitrarily weak optical lattice commensurate with the atomic granularity, which leads to immediate pinning of the atoms. We map out the phase diagram and find that our measurements in the strongly interacting regime agree well with a quantum field description based on the exactly solvable sineĝ€"Gordon model. We trace the phase boundary all the way to the weakly interacting regime, where we find good agreement with the predictions of the one-dimensional Boseĝ€"Hubbard model. Our results open up the experimental study of quantum phase transitions, criticality and transport phenomena beyond Hubbard-type models in the context of ultracold gases.}, author = {Haller, Elmar and Hart, Russell and Mark, Manfred and Danzl, Johann G and Reichsöllner, Lukas and Gustavsson, Mattias and Dalmonte, Marcello and Pupillo, Guido and Nägerl, Hanns}, journal = {Nature}, number = {7306}, pages = {597 -- 600}, publisher = {Nature Publishing Group}, title = {{Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons}}, doi = {10.1038/nature09259}, volume = {466}, year = {2010}, } @article{9452, abstract = {Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.}, author = {Zemach, Assaf and McDaniel, Ivy E. and Silva, Pedro and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5980}, pages = {916--919}, publisher = {American Association for the Advancement of Science}, title = {{Genome-wide evolutionary analysis of eukaryotic DNA methylation}}, doi = {10.1126/science.1186366}, volume = {328}, year = {2010}, } @article{9485, abstract = {Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.}, author = {Zemach, Assaf and Kim, M. Yvonne and Silva, Pedro and Rodrigues, Jessica A. and Dotson, Bradley and Brooks, Matthew D. and Zilberman, Daniel}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {43}, pages = {18729--18734}, publisher = {National Academy of Sciences}, title = {{Local DNA hypomethylation activates genes in rice endosperm}}, doi = {10.1073/pnas.1009695107}, volume = {107}, year = {2010}, } @article{9489, abstract = {Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.}, author = {Zemach, Assaf and Zilberman, Daniel}, issn = {1879-0445}, journal = {Current Biology}, number = {17}, pages = {R780--R785}, publisher = {Elsevier}, title = {{Evolution of eukaryotic DNA methylation and the pursuit of safer sex}}, doi = {10.1016/j.cub.2010.07.007}, volume = {20}, year = {2010}, } @misc{9764, author = {Rosas, Ulises and Barton, Nicholas H and Copsey, Lucy and Barbier De Reuille, Pierre and Coen, Enrico}, publisher = {Public Library of Science}, title = {{Heterosis and the drift load}}, doi = {10.1371/journal.pbio.1000429.s003}, year = {2010}, } @inproceedings{10908, abstract = {We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts.}, author = {Blanc, Régis and Henzinger, Thomas A and Hottelier, Thibaud and Kovács, Laura}, booktitle = {Logic for Programming, Artificial Intelligence, and Reasoning}, editor = {Clarke, Edmund M and Voronkov, Andrei}, isbn = {9783642175107}, issn = {1611-3349}, location = {Dakar, Senegal}, pages = {103--118}, publisher = {Springer Nature}, title = {{ABC: Algebraic Bound Computation for loops}}, doi = {10.1007/978-3-642-17511-4_7}, volume = {6355}, year = {2010}, } @inproceedings{10909, abstract = {We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.}, author = {Chen, Chao and Freedman, Daniel}, booktitle = {Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {Austin, TX, United States}, pages = {1594--1604}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Hardness results for homology localization}}, doi = {10.1137/1.9781611973075.129}, year = {2010}, } @article{11097, abstract = {The nuclear envelope (NE) is a highly regulated membrane barrier that separates the nucleus from the cytoplasm in eukaryotic cells. It contains a large number of different proteins that have been implicated in chromatin organization and gene regulation. Although the nuclear membrane enables complex levels of gene expression, it also poses a challenge when it comes to cell division. To allow access of the mitotic spindle to chromatin, the nucleus of metazoans must completely disassemble during mitosis, generating the need to re-establish the nuclear compartment at the end of each cell division. Here, I summarize our current understanding of the dynamic remodeling of the NE during the cell cycle.}, author = {HETZER, Martin W}, issn = {1943-0264}, journal = {Cold Spring Harbor Perspectives in Biology}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {3}, pages = {a000539--a000539}, publisher = {Cold Spring Harbor Laboratory}, title = {{The nuclear envelope}}, doi = {10.1101/cshperspect.a000539}, volume = {2}, year = {2010}, } @article{11098, author = {HETZER, Martin W}, issn = {1945-4589}, journal = {Aging}, keywords = {Cell Biology, Aging}, number = {2}, pages = {74--75}, publisher = {Impact Journals}, title = {{The role of the nuclear pore complex in aging of post-mitotic cells}}, doi = {10.18632/aging.100125}, volume = {2}, year = {2010}, } @article{11099, abstract = {Nuclear pore complexes (NPCs) serve as transport channels across the nuclear membrane, a double lipid bilayer that physically separates the nucleoplasm and cytoplasm of eukaryotic cells. New evidence suggests that the multiprotein nuclear pores also play a role in chromatin organization and gene expression. Given the importance of NPC function, it is not surprising that a growing list of human diseases and developmental defects have been linked to its malfunction. In order to fully understand the functional repertoire of NPCs and their essential role for nuclear organization, it is critical to determine the sequence of events that lead to the formation of nuclear pores. This is particularly relevant since NPC number, and possibly composition, are tightly linked to metabolic activity. Most of our knowledge is derived from NPC formation that occurs in dividing cells at the end of mitosis when the nuclear envelope (NE) and NPCs reform from disassembled precursors. However, NPC assembly also takes place during interphase into an intact NE. Importantly, this process is not restricted to dividing cells but also occurs during cell differentiation. Here, we will review aspects unique to this process, namely the regulation of nuclear expansion and the mechanisms of fusion between the outer and inner nuclear membranes. We will then discuss conserved and diverging mechanisms between post-mitotic and interphase assembly of the proteinaceous structure in light of recently published data.}, author = {Doucet, Christine M. and HETZER, Martin W}, issn = {1432-0886}, journal = {Chromosoma}, keywords = {Genetics (clinical), Genetics}, pages = {469--477}, publisher = {Springer Nature}, title = {{Nuclear pore biogenesis into an intact nuclear envelope}}, doi = {10.1007/s00412-010-0289-2}, volume = {119}, year = {2010}, } @article{11101, abstract = {In metazoa, nuclear pore complexes (NPCs) assemble from disassembled precursors into a reforming nuclear envelope (NE) at the end of mitosis and into growing intact NEs during interphase. Here, we show via RNAi-mediated knockdown that ELYS, a nucleoporin critical for the recruitment of the essential Nup107/160 complex to chromatin, is required for NPC assembly at the end of mitosis but not during interphase. Conversely, the transmembrane nucleoporin POM121 is critical for the incorporation of the Nup107/160 complex into new assembly sites specifically during interphase. Strikingly, recruitment of the Nup107/160 complex to an intact NE involves a membrane curvature-sensing domain of its constituent Nup133, which is not required for postmitotic NPC formation. Our results suggest that in organisms with open mitosis, NPCs assemble via two distinct mechanisms to accommodate cell cycle-dependent differences in NE topology.}, author = {Doucet, Christine M. and Talamas, Jessica A. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {6}, pages = {1030--1041}, publisher = {Elsevier}, title = {{Cell cycle-dependent differences in nuclear pore complex assembly in metazoa}}, doi = {10.1016/j.cell.2010.04.036}, volume = {141}, year = {2010}, } @article{11102, abstract = {Nuclear pore complexes have recently been shown to play roles in gene activation; however their potential involvement in metazoan transcription remains unclear. Here we show that the nucleoporins Sec13, Nup98, and Nup88, as well as a group of FG-repeat nucleoporins, bind to the Drosophila genome at functionally distinct loci that often do not represent nuclear envelope contact sites. Whereas Nup88 localizes to silent loci, Sec13, Nup98, and a subset of FG-repeat nucleoporins bind to developmentally regulated genes undergoing transcription induction. Strikingly, RNAi-mediated knockdown of intranuclear Sec13 and Nup98 specifically inhibits transcription of their target genes and prevents efficient reactivation of transcription after heat shock, suggesting an essential role of NPC components in regulating complex gene expression programs of multicellular organisms.}, author = {Capelson, Maya and Liang, Yun and Schulte, Roberta and Mair, William and Wagner, Ulrich and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {3}, pages = {372--383}, publisher = {Elsevier}, title = {{Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes}}, doi = {10.1016/j.cell.2009.12.054}, volume = {140}, year = {2010}, } @inproceedings{11753, abstract = {Ferroelectric ceramic materials have a wide range of applications because of their piezoelectric and pyroelectric properties. One of their most important physical properties is the specific heat. In this study, the specific heats of a series of lead-zirconate-titanate (PZT) compositions in the vicinity of the morphotropic phase boundary (MPB) were measured. The temperature range was from 1.8 to 300 K. It is believed that these are the lowest temperature measurements ever made on PZT. Differences between the specific heats of the different compositions were very small. However, the calculated Debye temperatures were slightly different. The results are useful in computing design parameters for technical devices.}, author = {Lang, S. B. and Lashley, J. C. and Modic, Kimberly A and Fisher, R. A. and Zhu, W. M. and Ye, Z. G.}, booktitle = {Proceedings of the 2010 IEEE International Conference on Solid Dielectrics}, issn = {2159-1687}, location = {Potsdam, Germany}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary}}, doi = {10.1109/icsd.2010.5568033}, year = {2010}, } @inproceedings{11754, abstract = {Ferroelectric ceramic materials have a wide range of applications because of their piezoelectric and pyroelectric properties. One of their most important physical properties is the specific heat. In this study, the specific heats of a series of lead-zirconate-titanate (PZT) compositions in the vicinity of the morphotropic phase boundary (MPB) were measured. The temperature range was from 1.8 to 300 K. It is believed that these are the lowest temperature measurements ever made on PZT. Differences between the specific heats of the different compositions were very small. However, the calculated Debye temperatures were slightly different. The results are useful in computing design parameters for technical devices.}, author = {Lang, S.B. and Lashley, J.C. and Modic, Kimberly A and Fisher, R.A. and Zhu, W.M. and Ye, Z.G.}, booktitle = {15th IEEE Mediterranean Electrotechnical Conference}, isbn = {978-142445795-3}, location = {Valletta, Malta}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary}}, doi = {10.1109/melcon.2010.5476345}, year = {2010}, } @inproceedings{11797, abstract = {Inspired by online ad allocation, we study online stochastic packing integer programs from theoretical and practical standpoints. We first present a near-optimal online algorithm for a general class of packing integer programs which model various online resource allocation problems including online variants of routing, ad allocations, generalized assignment, and combinatorial auctions. As our main theoretical result, we prove that a simple dual training-based algorithm achieves a (1 − o(1))-approximation guarantee in the random order stochastic model. This is a significant improvement over logarithmic or constant-factor approximations for the adversarial variants of the same problems (e.g. factor 1−1𝑒 for online ad allocation, and log(m) for online routing). We then focus on the online display ad allocation problem and study the efficiency and fairness of various training-based and online allocation algorithms on data sets collected from real-life display ad allocation system. Our experimental evaluation confirms the effectiveness of training-based algorithms on real data sets, and also indicates an intrinsic trade-off between fairness and efficiency.}, author = {Feldman, Jon and Henzinger, Monika H and Korula, Nitish and Mirrokni, Vahab S. and Stein, Cliff}, booktitle = {18th Annual European Symposium on Algorithms}, isbn = {3642157742}, issn = {1611-3349}, location = {Liverpool, United Kingdom}, pages = {182–194}, publisher = {Springer Nature}, title = {{Online stochastic packing applied to display ad allocation}}, doi = {10.1007/978-3-642-15775-2_16}, volume = {6346}, year = {2010}, }