@article{1763, abstract = {The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.}, author = {Johannes Fink and Göppl, M and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Nature}, number = {7202}, pages = {315 -- 318}, publisher = {Nature Publishing Group}, title = {{Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system}}, doi = {10.1038/nature07112}, volume = {454}, year = {2008}, } @article{1764, abstract = {Quantum theory predicts that empty space is not truly empty. Even in the absence of any particles or radiation, in pure vacuum, virtual particles are constantly created and annihilated. In an electromagnetic field, the presence of virtual photons manifests itself as a small renormalization of the energy of a quantum system, known as the Lamb shift. We present an experimental observation of the Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition frequency. The qubit is also observed to couple more strongly to the vacuum field than to a single photon inside the cavity, an effect that is explained by taking into account the limited anharmonicity of the higher excited qubit states.}, author = {Fragner, A and Göppl, M and Johannes Fink and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Science}, number = {5906}, pages = {1357 -- 1360}, publisher = {American Association for the Advancement of Science}, title = {{Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift}}, doi = {10.1126/science.1164482}, volume = {322}, year = {2008}, } @article{1765, abstract = {High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.}, author = {Göppl, M and Fragner, A and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Johannes Fink and Leek, Peter J and Puebla, G and Steffen, L. Kraig and Wallraff, Andreas}, journal = {Journal of Applied Physics}, number = {11}, publisher = {American Institute of Physics}, title = {{Coplanar waveguide resonators for circuit quantum electrodynamics}}, doi = {10.1063/1.3010859}, volume = {104}, year = {2008}, } @article{1826, abstract = {Proliferating cell populations at steady-state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by asymptotic analysis of the population balance equation. We show that the steady-state distribution tail is determined by a combination of protein production and cell division and is insensitive to other model details. Under general conditions this tail is exponential with a dependence on parameters consistent with experiment. We discuss the conditions for this effect to be dominant over other sources of variation and the relation to experiments.}, author = {Tamar Friedlander and Brenner, Naama}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Cellular properties and population asymptotics in the population balance equation}}, doi = {10.1103/PhysRevLett.101.018104}, volume = {101}, year = {2008}, } @article{1967, abstract = {Complex I of respiratory chains transfers electrons from NADH to ubiquinone, coupled to the translocation of protons across the membrane. Two alternative coupling mechanisms are being discussed, redox-driven or conformation-driven. Using "zero-length" cross-linking reagent and isolated hydrophilic domains of complex I from Escherichia coli and Thermus thermophilus, we show that the pattern of cross-links between subunits changes significantly in the presence of NADH. Similar observations were made previously with intact purified E. coli and bovine complex I. This indicates that, upon reduction with NADH, similar conformational changes are likely to occur in the intact enzyme and in the isolated hydrophilic domain (which can be used for crystallographic studies). Within intact E. coli complex I, the cross-link between the hydrophobic subunits NuoA and NuoJ was abolished in the presence of NADH, indicating that conformational changes extend into the membrane domain, possibly as part of a coupling mechanism. Unexpectedly, in the absence of any chemical cross-linker, incubation of complex I with NADH resulted in covalent cross-links between subunits Nqo4 (NuoCD) and Nqo6 (NuoB), as well as between Nqo6 and Nqo9. Their formation depends on the presence of oxygen and so is likely a result of oxidative damage via reactive oxygen species (ROS) induced cross-linking. In addition, ROS- and metal ion-dependent proteolysis of these subunits (as well as Nqo3) is observed. Fe-S cluster N2 is coordinated between subunits Nqo4 and Nqo6 and could be involved in these processes. Our observations suggest that oxidative damage to complex I in vivo may include not only side-chain modifications but also protein cross-linking and degradation.}, author = {Berrisford, John M and Thompson, Christopher J and Leonid Sazanov}, journal = {Biochemistry}, number = {39}, pages = {10262 -- 10270}, publisher = {ACS}, title = {{Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus}}, doi = {10.1021/bi801160u}, volume = {47}, year = {2008}, } @article{1968, abstract = { Complex I (NADH:ubiquinone oxidoreductase) is the largest protein complex of bacterial and mitochondrial respiratory chains. The first three-dimensional structure of bacterial complex I in vitrified ice was determined by electron cryo-microscopy and single particle analysis. The structure of the Escherichia coli enzyme incubated with either NAD+ (as a reference) or NADH was calculated to 35 and 39 Å resolution, respectively. The X-ray structure of the peripheral arm of Thermus thermophilus complex I was docked into the reference EM structure. The model obtained indicates that Fe-S cluster N2 is close to the membrane domain interface, allowing for effective electron transfer to membrane-embedded quinone. At the current resolution, the structures in the presence of NAD+ or NADH are similar. Additionally, side-view class averages were calculated for the negatively stained bovine enzyme. The structures of bovine complex I in the presence of either NAD+ or NADH also appeared to be similar. These observations indicate that conformational changes upon reduction with NADH, suggested to occur by a range of studies, are smaller than had been thought previously. The model of the entire bacterial complex I could be built from the crystal structures of subcomplexes using the EM envelope described here.}, author = {Morgan, David J and Leonid Sazanov}, journal = {Biochimica et Biophysica Acta - Bioenergetics}, number = {7-8}, pages = {711 -- 718}, publisher = {Elsevier}, title = {{Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides}}, doi = {10.1016/j.bbabio.2008.03.023}, volume = {1777}, year = {2008}, } @article{1982, abstract = {In the bacterium Escherichia coli, the Min proteins oscillate between the cell poles to select the cell center as division site. This dynamic pattern has been proposed to arise by self-organization of these proteins, and several models have suggested a reaction-diffusion type mechanism. Here, we found that the Min proteins spontaneously formed planar surface waves on a flat membrane in vitro. The formation and maintenance of these patterns, which extended for hundreds of micrometers, required adenosine 5′-triphosphate (ATP), and they persisted for hours. We present a reaction-diffusion model of the MinD and MinE dynamics that accounts for our experimental observations and also captures the in vivo oscillations.}, author = {Martin Loose and Fischer-Friedrich, Elisabeth and Ries, Jonas and Kruse, Karsten and Schwille, Petra }, journal = {Science}, number = {5877}, pages = {789 -- 792}, publisher = {American Association for the Advancement of Science}, title = {{Spatial regulators for bacterial cell division self-organize into surface waves in vitro}}, doi = {10.1126/science.1154413}, volume = {320}, year = {2008}, } @article{2065, abstract = {Population genetics models show that, under certain conditions, the X chromosome is expected to be under more efficient selection than the autosomes. This could lead to 'faster-X evolution', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in Drosophila. We used a multispecies approach to test this: Muller's element D, an autosomal arm, is fused to the ancestral X chromosome in Drosophila pseudoobscura and its sister species, Drosophila affinis. We tested whether the same set of genes had higher rates of non-synonymous evolution when they were X-linked (in the D. pseudoobscura/D. affinis comparison) than when they were autosomal (in Drosophila melanogaster/Drosophila yakuba). Although not significant, our results suggest this may be the case, but only for genes under particularly strong positive selection/weak purifying selection. They also suggest that genes that have become X-linked have higher levels of codon bias and slower synonymous site evolution, consistent with more effective selection on codon usage at X-linked sites.}, author = {Beatriz Vicoso and Haddrill, Penelope R and Charlesworth, Brian}, journal = {Genetical Research}, number = {5}, pages = {421 -- 431}, publisher = {Cambridge University Press}, title = {{A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila}}, doi = {10.1017/S0016672308009804}, volume = {90}, year = {2008}, } @article{13422, abstract = {Make like a leaf: The synthesis and characterization of a family of “flowerlike” Au/Fe3O4 nanoparticles is described, whereby Fe3O4 “leaves” adhere to a gold core (see image). The size and numbers of iron oxide domains can be adjusted flexibly by changing the proportion of the starting materials and the reaction time.}, author = {Wei, Yanhu and Klajn, Rafal and Pinchuk, Anatoliy O. and Grzybowski, Bartosz A.}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {10}, pages = {1635--1639}, publisher = {Wiley}, title = {{Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”}}, doi = {10.1002/smll.200800511}, volume = {4}, year = {2008}, } @article{13423, abstract = {Supraspheres (SS) composed of hundreds to thousands of metal nanoparticles (NPs) and crosslinked by dithiol linkers are assembled into larger structures, which are subsequently converted into nanoporous metals (NMs). Conversion is achieved by heating which removes organic molecules stabilizing the NPs and allows for NP fusion. Heating of SS solutions leads to NMs of overall macroscopic dimensions; localized radiation using collimated electron beam is used to prepare metallized surface micropatterns. Depending on the composition of supraspherical precursors, nanoporous materials composed of up to three metals can be obtained. Strategies for controlling pore size and nanoscale surface roughness of these materials are discussed.}, author = {Klajn, Rafal and Gray, Timothy P. and Wesson, Paul J. and Myers, Benjamin D. and Dravid, Vinayak P. and Smoukov, Stoyan K. and Grzybowski, Bartosz A.}, issn = {1616-3028}, journal = {Advanced Functional Materials}, keywords = {Electrochemistry, Condensed Matter Physics, Biomaterials, Electronic, Optical and Magnetic Materials}, number = {18}, pages = {2763--2769}, publisher = {Wiley}, title = {{Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates}}, doi = {10.1002/adfm.200800293}, volume = {18}, year = {2008}, } @article{1460, abstract = {We calculate the E-polynomials of certain twisted GL(n,ℂ)-character varieties Mn of Riemann surfaces by counting points over finite fields using the character table of the finite group of Lie-type GL(n, q) and a theorem proved in the appendix by N. Katz. We deduce from this calculation several geometric results, for example, the value of the topological Euler characteristic of the associated PGL(n,ℂ)-character variety. The calculation also leads to several conjectures about the cohomology of Mn: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable representations of a certain quiver. We prove these conjectures for n=2.}, author = {Tamas Hausel and Rodríguez Villegas, Fernando}, journal = {Inventiones Mathematicae}, number = {3}, pages = {555 -- 624}, publisher = {Springer}, title = {{Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz}}, doi = {10.1007/s00222-008-0142-x}, volume = {174}, year = {2008}, } @article{581, abstract = {We have detected a spin-dependent displacement perpendicular to the refractive index gradient for photons passing through an air-glass interface. The effect is the photonic version of the spin Hall effect in electronic systems, indicating the universality of the effect for particles of different nature. Treating the effect as a weak measurement of the spin projection of the photons, we used a preselection and postselection technique on the spin state to enhance the original displacement by nearly four orders of magnitude, attaining sensitivity to displacements of ∼1 angstrom. The spin Hall effect can be used for manipulating photonic angular momentum states, and the measurement technique holds promise for precision metrology.}, author = {Onur Hosten and Kwiat, Paul}, journal = {Science}, number = {5864}, pages = {787 -- 790}, publisher = {American Association for the Advancement of Science}, title = {{Observation of the spin hall effect of light via weak measurements}}, doi = {10.1126/science.1152697}, volume = {319}, year = {2008}, } @inproceedings{584, abstract = {Using “quantum weak-measurements” as a coherent enhancement technique for small signals, we have measured the recently proposed “spin Hall effect” of light at an air-glass interface, and are working on the smoothly varying refractive-index case.}, author = {Hosten, Onur and Kwiat, Paul}, isbn = {978-155752859-9}, issn = {21622701}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Spin hall effect of light via weak measurements: Sharp and smooth index variations}}, year = {2008}, } @article{6146, abstract = {Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies.}, author = {Bretscher, A. J. and Busch, K. E. and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {8044--8049}, publisher = {Proceedings of the National Academy of Sciences}, title = {{A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans}}, doi = {10.1073/pnas.0707607105}, volume = {105}, year = {2008}, } @article{6148, author = {Kammenga, Jan E. and Phillips, Patrick C. and de Bono, Mario and Doroszuk, Agnieszka}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {4}, pages = {178--185}, publisher = {Elsevier}, title = {{Beyond induced mutants: using worms to study natural variation in genetic pathways}}, doi = {10.1016/j.tig.2008.01.001}, volume = {24}, year = {2008}, } @article{6149, author = {Olofsson, Birgitta and de Bono, Mario}, issn = {0960-9822}, journal = {Current Biology}, number = {5}, pages = {R204--R206}, publisher = {Elsevier}, title = {{Sleep: dozy worms and sleepy flies}}, doi = {10.1016/j.cub.2008.01.002}, volume = {18}, year = {2008}, } @article{1036, abstract = {We report on the control of interaction-induced dephasing of Bloch oscillations for an atomic Bose-Einstein condensate in an optical lattice. We quantify the dephasing in terms of the width of the quasimomentum distribution and measure its dependence on time for different interaction strengths which we control by means of a Feshbach resonance. For minimal interaction, the dephasing time is increased from a few to more than 20 thousand Bloch oscillation periods, allowing us to realize a BEC-based atom interferometer in the noninteracting limit.}, author = {Gustavsson, Mattias and Haller, Elmar and Mark, Manfred and Danzl, Johann G and Rojas Kopeinig, Gabriel and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Control of interaction-induced dephasing of bloch oscillations}}, doi = {10.1103/PhysRevLett.100.080404}, volume = {100}, year = {2008}, } @article{1037, abstract = {We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation threshold, which are stable against spontaneous decay on the time scale of 1s. An optically trapped sample of ultracold dimers is prepared in a high rotational state and magnetically tuned into a region with a negative binding energy. The metastable character of these molecules arises from the large centrifugal barrier in combination with negligible coupling to states with low rotational angular momentum. A sharp onset of dissociation with increasing magnetic field is mediated by a crossing with a lower rotational dimer state and facilitates dissociation on demand with a well-defined energy.}, author = {Knoop, Steven and Mark, Michael and Ferlaino, Francesca and Danzl, Johann G and Kraemer, Tobias and Nägerl, Hanns and Grimm, Rudolf}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Metastable feshbach molecules in high rotational states}}, doi = {10.1103/PhysRevLett.100.083002}, volume = {100}, year = {2008}, } @article{1039, abstract = {Molecular cooling techniques face the hurdle of dissipating translational as well as internal energy in the presence of a rich electronic, vibrational, and rotational energy spectrum. In our experiment, we create a translationally ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers in the electronic ground state. Specifically, we stimulate with 80% efficiency, a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein condensate of cesium atoms. In the process, the initial loose, long-range electrostatic bond of the Feshbach molecule is coherently transformed into a tight chemical bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and show that the molecular sample is not heated during the transfer. Our results show that the preparation of a quantum gas of molecules in specific rovibrational states is possible and that the creation of a Bose-Einstein condensate of molecules in their rovibronic ground state is within reach.}, author = {Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Hart, Russell and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Nägerl, Hanns}, journal = {Science}, number = {5892}, pages = {1062 -- 1066}, publisher = {American Association for the Advancement of Science}, title = {{Quantum gas of deeply bound ground state molecules}}, doi = {10.1126/science.1159909}, volume = {321}, year = {2008}, } @article{10392, abstract = {Protonated formylmetallocenes [M(C5H5)(C5H4-CHOH)]+ (M = Fe, Ru) and their isomers have been studied at the BP86 and B3LYP levels of density functional theory. Oxygen-protonated isomers are the most stable forms in each case, with a plethora of ring- or metal-protonated species at least ca. 14 and 10 kcal/mol higher in energy for M = Fe and Ru, respectively. The computed rotational barriers around the C−C bond connecting the cyclopentadienyl and protonated formyl moieties, ca. 18 kcal/mol, are indicative of substantial conjugation between these moieties. Some of the ring- and iron-protonated species are models for possible intermediates in Friedel–Crafts acylation of ferrocene, and the computations provide further evidence that exo attack is clearly favored over endo attack of the electrophile in this reaction. The structures of the most stable mono- and diprotonated formylferrocenes are corroborated by the good agreement between GIAO-B3LYP-computed and experimental NMR chemical shifts.}, author = {Šarić, Anđela and Vrček, Valerije and Bühl, Michael}, issn = {1520-6041}, journal = {Organometallics}, keywords = {Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry}, number = {3}, pages = {394--401}, publisher = {American Chemical Society}, title = {{Density functional study of protonated formylmetallocenes}}, doi = {10.1021/om700916f}, volume = {27}, year = {2008}, }