TY - JOUR AB - An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand. AU - Šarić, Anđela AU - Hrenar, T. AU - Mališ, M. AU - Došlić, N. ID - 10128 IS - 18 JF - Physical Chemistry Chemical Physics KW - Physical and Theoretical Chemistry KW - General Physics and Astronomy SN - 1463-9076 TI - Quantum mechanical study of secondary structure formation in protected dipeptides VL - 12 ER - TY - JOUR AB - We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results. AU - Šarić, Anđela AU - Cacciuto, Angelo ID - 10127 IS - 5 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Particle self-assembly on soft elastic shells VL - 7 ER - TY - JOUR AB - We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases, which includes most of the mesophases observed in self-assembly of block copolymers but also crystalline structures formed by asymmetric, hard binary mixtures. Our results detail the phenomenological behavior of these systems when softness is introduced in terms of two different classes of interparticle interactions: (a) the elastic Hertz potential, which has a finite energy cost for complete overlap of any two components, and (b) a generic power-law repulsion with tunable exponent. We discuss how simple geometric arguments can be used to account for the large structural variety observed in these systems and detail the similarities and differences in the phase behavior for the two classes of potentials under consideration. AU - Šarić, Anđela AU - Bozorgui, Behnaz AU - Cacciuto, Angelo ID - 10390 IS - 22 JF - The Journal of Physical Chemistry B KW - materials chemistry SN - 1520-6106 TI - Packing of soft asymmetric dumbbells VL - 115 ER - TY - JOUR AB - We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results. AU - Šarić, Anđela AU - Pàmies, Josep C. AU - Cacciuto, Angelo ID - 10391 IS - 22 JF - Physical Review Letters KW - general physics and astronomy SN - 0031-9007 TI - Effective elasticity of a flexible filament bound to a deformable cylindrical surface VL - 104 ER - TY - CONF AB - 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. AU - Danzl, Johann G AU - Mark, Manfred AU - Haller, Elmar AU - Gustavsson, Mattias AU - Hart, Russell AU - Nägerl, Hanns ID - 1042 TI - Production of a quantum gas of rovibronic ground-state molecules in an optical lattice ER - TY - JOUR AB - 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. AU - Danzl, Johann G AU - Mark, Manfred AU - Haller, Elmar AU - Gustavsson, Mattias AU - Hart, Russell AU - Aldegunde, Jesus AU - Hutson, Jeremy AU - Nägerl, Hanns ID - 1044 IS - 4 JF - Nature Physics TI - An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice VL - 6 ER - TY - JOUR AB - 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. AU - Haller, Elmar AU - Mark, Manfred AU - Hart, Russell AU - Danzl, Johann G AU - Reichsöllner, Lukas AU - Melezhik, Vladimir AU - Schmelcher, Peter AU - Nägerl, Hanns ID - 1045 IS - 15 JF - Physical Review Letters TI - Confinement-induced resonances in low-dimensional quantum systems VL - 104 ER - TY - JOUR AB - 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. AU - Haller, Elmar AU - Hart, Russell AU - Mark, Manfred AU - Danzl, Johann G AU - Reichsöllner, Lukas AU - Gustavsson, Mattias AU - Dalmonte, Marcello AU - Pupillo, Guido AU - Nägerl, Hanns ID - 1049 IS - 7306 JF - Nature TI - Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons VL - 466 ER - TY - JOUR AB - 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. AU - Haller, Elmar AU - Hart, Russell AU - Mark, Manfred AU - Danzl, Johann G AU - Reichsöllner, Lukas AU - Nägerl, Hanns ID - 1047 IS - 20 JF - Physical Review Letters TI - Inducing transport in a dissipation-free lattice with super bloch oscillations VL - 104 ER - TY - JOUR AB - 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. AU - Gustavsson, Mattias AU - Haller, Elmar AU - Mark, Manfred AU - Danzl, Johann G AU - Hart, Russell AU - Daley, Andrew AU - Nägerl, Hanns ID - 1046 JF - New Journal of Physics TI - Interference of interacting matter waves VL - 12 ER - TY - CONF AB - 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. AU - Blanc, Régis AU - Henzinger, Thomas A AU - Hottelier, Thibaud AU - Kovács, Laura ED - Clarke, Edmund M ED - Voronkov, Andrei ID - 10908 SN - 0302-9743 T2 - Logic for Programming, Artificial Intelligence, and Reasoning TI - ABC: Algebraic Bound Computation for loops VL - 6355 ER - TY - JOUR AB - 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. AU - HETZER, Martin W ID - 11097 IS - 3 JF - Cold Spring Harbor Perspectives in Biology KW - General Biochemistry KW - Genetics and Molecular Biology SN - 1943-0264 TI - The nuclear envelope VL - 2 ER - TY - JOUR AB - 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. AU - Doucet, Christine M. AU - HETZER, Martin W ID - 11099 JF - Chromosoma KW - Genetics (clinical) KW - Genetics SN - 0009-5915 TI - Nuclear pore biogenesis into an intact nuclear envelope VL - 119 ER - TY - JOUR AB - 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. AU - Capelson, Maya AU - Liang, Yun AU - Schulte, Roberta AU - Mair, William AU - Wagner, Ulrich AU - HETZER, Martin W ID - 11102 IS - 3 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes VL - 140 ER - TY - JOUR AB - 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. AU - Doucet, Christine M. AU - Talamas, Jessica A. AU - HETZER, Martin W ID - 11101 IS - 6 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Cell cycle-dependent differences in nuclear pore complex assembly in metazoa VL - 141 ER - TY - JOUR AU - HETZER, Martin W ID - 11098 IS - 2 JF - Aging KW - Cell Biology KW - Aging SN - 1945-4589 TI - The role of the nuclear pore complex in aging of post-mitotic cells VL - 2 ER - TY - CONF AB - 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. AU - Lang, S. B. AU - Lashley, J. C. AU - Modic, Kimberly A AU - Fisher, R. A. AU - Zhu, W. M. AU - Ye, Z. G. ID - 11753 SN - 1553-5282 T2 - Proceedings of the 2010 IEEE International Conference on Solid Dielectrics TI - Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary ER - TY - CONF AB - 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. AU - Lang, S.B. AU - Lashley, J.C. AU - Modic, Kimberly A AU - Fisher, R.A. AU - Zhu, W.M. AU - Ye, Z.G. ID - 11754 SN - 978-142445795-3 T2 - 15th IEEE Mediterranean Electrotechnical Conference TI - Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary ER - TY - CONF AB - 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. AU - Feldman, Jon AU - Henzinger, Monika H AU - Korula, Nitish AU - Mirrokni, Vahab S. AU - Stein, Cliff ID - 11797 SN - 1611-3349 T2 - 18th Annual European Symposium on Algorithms TI - Online stochastic packing applied to display ad allocation VL - 6346 ER - TY - CONF AB - Starting with two models fifty years ago, the discrete marriage game [1] and the continuous assignment game [2], the study of stable matchings has evolved into a rich theory with applications in many areas. Most notably, it has lead to a number of truthful mechanisms that have seen a recent rejuvenation in the context of sponsored search. In this paper we survey the history of these problems and provide several links to ongoing research in the field. AU - Dütting, Paul AU - Henzinger, Monika H ID - 11798 SN - 1611-3349 T2 - 7th International Conference on Algorithms and Complexity TI - Mechanisms for the marriage and the assignment game VL - 6078 ER -