@article{1717, abstract = {Two key processes are in the basis of morphogenesis: the spatial allocation of cell types in fields of naïve cells and the regulation of growth. Both are controlled by morphogens, which activate target genes in the growing tissue in a concentration-dependent manner. Thus the morphogen model is an intrinsically quantitative concept. However, quantitative studies were performed only in recent years on two morphogens: Bicoid and Decapentaplegic. This review covers quantitative aspects of the formation and precision of the Decapentaplegic morphogen gradient. The morphogen gradient concept is transitioning from a soft definition to a precise idea of what the gradient could really do.}, author = {Anna Kicheva and González-Gaitán, Marcos A}, journal = {Current Opinion in Cell Biology}, number = {2}, pages = {137 -- 143}, publisher = {Elsevier}, title = {{The Decapentaplegic morphogen gradient a precise definition}}, doi = {10.1016/j.ceb.2008.01.008}, volume = {20}, year = {2008}, } @article{1719, abstract = {We study the mechanics of tissue growth via cell division and cell death (apoptosis). The rearrangements of cells can on large scales and times be captured by a continuum theory which describes the tissue as an effective viscous material with active stresses generated by cell division. We study the effects of anisotropies of cell division on cell rearrangements and show that average cellular trajectories exhibit anisotropic scaling behaviors. If cell division and apoptosis balance, there is no net growth, but for anisotropic cell division the tissue undergoes spontaneous shear deformations. Our description is relevant for the study of developing tissues such as the imaginal disks of the fruit fly Drosophila melanogaster, which grow anisotropically.}, author = {Bittig, Thomas and Wartlick, Ortrud and Anna Kicheva and González-Gaitárr, Marcos and Julicher, Frank}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Dynamics of anisotropic tissue growth}}, doi = {10.1088/1367-2630/10/6/063001}, volume = {10}, year = {2008}, } @article{1749, abstract = {Scanning probe microscopy; Semiconductor quantum dots; Composition gradients; Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional (3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology; nanotechnology; optical tomography; scanning probe microscopy; three dimensional imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe; Nanotechnology; Quantum Dots; Tomography,}, author = {Rastelli, Armando and Stoffel, Mathieu and Malachias, Ângelo S and Merdzhanova, Tsvetelina and Georgios Katsaros and Kern, Klaus and Metzger, Till H and Schmidt, Oliver G}, journal = {Nano Letters}, number = {5}, pages = {1404 -- 1409}, publisher = {American Chemical Society}, title = {{Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography}}, doi = {10.1021/nl080290y}, volume = {8}, year = {2008}, } @article{1751, abstract = {When strained Stranski-Krastanow islands are used as "self-assembled quantum dots," a key goal is to control the island position. Here we show that nanoscale grooves can control the nucleation of epitaxial Ge islands on Si(001), and can drive lateral motion of existing islands onto the grooves, even when the grooves are very narrow and shallow compared to the islands. A position centered on the groove minimizes energy. We use as prototype grooves the trenches which form naturally around islands. During coarsening, the shrinking islands move laterally to sit directly astride that trench. In subsequent growth, we demonstrate that islands nucleate on the "empty trenches" which remain on the surface after complete dissolution of the original islands.}, author = {Georgios Katsaros and Tersoff, Jerry and Stoffel, Mathieu and Rastelli, Armando and Acosta-Diaz, P and Kar, Gouranga S and Costantini, Giovanni and Schmidt, Oliver G and Kern, Klaus}, journal = {Physical Review Letters}, number = {9}, publisher = {American Physical Society}, title = {{Positioning of strained islands by interaction with surface nanogrooves}}, doi = {10.1103/PhysRevLett.101.096103}, volume = {101}, year = {2008}, } @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}, } @inproceedings{2078, abstract = {This paper presents a novel method for real-time animation of highly-detailed facial expressions based on a multi-scale decomposition of facial geometry into large-scale motion and fine-scale details, such as expression wrinkles. Our hybrid animation is tailored to the specific characteristics of large- and fine-scale facial deformations: Large-scale deformations are computed with a fast linear shell model, which is intuitively and accurately controlled through a sparse set of motion-capture markers or user-defined handle points. Fine-scale facial details are incorporated using a novel pose-space deformation technique, which learns the correspondence of sparse measurements of skin strain to wrinkle formation from a small set of example poses. Our hybrid method features real-time animation of highly-detailed faces with realistic wrinkle formation, and allows both large-scale deformations and fine-scale wrinkles to be edited intuitively. Furthermore, our pose-space representation enables the transfer of facial details to novel expressions or other facial models.}, author = {Bickel, Bernd and Lang, Manuel and Botsch, Mario and Otaduy, Miguel and Gross, Markus}, pages = {57 -- 66}, publisher = {ACM}, title = {{Pose-space animation and transfer of facial details}}, doi = {10.2312/SCA/SCA08/057-066}, year = {2008}, } @article{2120, abstract = {We consider the linear stochastic Cauchy problem dX (t) =AX (t) dt +B dWH (t), t≥ 0, where A generates a C0-semigroup on a Banach space E, WH is a cylindrical Brownian motion over a Hilbert space H, and B: H → E is a bounded operator. Assuming the existence of a unique minimal invariant measure μ∞, let Lp denote the realization of the Ornstein-Uhlenbeck operator associated with this problem in Lp (E, μ∞). Under suitable assumptions concerning the invariance of the range of B under the semigroup generated by A, we prove the following domain inclusions, valid for 1 < p ≤ 2: Image omitted. Here WHk, p (E, μinfin; denotes the kth order Sobolev space of functions with Fréchet derivatives up to order k in the direction of H. No symmetry assumptions are made on L p.}, author = {Jan Maas and van Neerven, Jan M}, journal = {Infinite Dimensional Analysis, Quantum Probability and Related Topics}, number = {4}, pages = {603 -- 626}, publisher = {World Scientific Publishing}, title = {{On the domain of non-symmetric Ornstein-Uhlenbeck operators in banach spaces}}, doi = {10.1142/S0219025708003245}, volume = {11}, year = {2008}, } @article{2121, abstract = {Let H be a separable real Hubert space and let double struck F sign = (ℱt)t∈[0,T] be the augmented filtration generated by an H-cylindrical Brownian motion (WH(t))t∈[0,T] on a probability space (Ω, ℱ ℙ). We prove that if E is a UMD Banach space, 1 ≤ p < ∞, and F ∈ double struck D sign1,p(Ω E) is ℱT-measurable, then F = double struck E sign(F) + ∫0T Pdouble struck F sign(DF) dW H, where D is the Malliavin derivative of F and P double struck F sign is the projection onto the F-adapted elements in a suitable Banach space of Lp-stochastically integrable ℒ(H, E)-valued processes.}, author = {van Neerven, Jan M and Jan Maas}, journal = {Electronic Communications in Probability}, pages = {151 -- 164}, publisher = {Institute of Mathematical Statistics}, title = {{A Clark-Ocone formula in UMD Banach spaces}}, volume = {13}, year = {2008}, } @article{2146, abstract = {We present an analytic model of thermal state-to-state rotationally inelastic collisions of polar molecules in electric fields. The model is based on the Fraunhofer scattering of matter waves and requires Legendre moments characterizing the “shape” of the target in the body-fixed frame as its input. The electric field orients the target in the space-fixed frame and thereby effects a striking alteration of the dynamical observables: both the phase and amplitude of the oscillations in the partial differential cross sections undergo characteristic field-dependent changes that transgress into the partial integral cross sections. As the cross sections can be evaluated for a field applied parallel or perpendicular to the relative velocity, the model also offers predictions about steric asymmetry. We exemplify the field-dependent quantum collision dynamics with the behavior of the Ne–OCS(Σ1) and Ar–NO(Π2) systems. A comparison with the close-coupling calculations available for the latter system [Chem. Phys. Lett.313, 491 (1999)] demonstrates the model’s ability to qualitatively explain the field dependence of all the scattering features observed.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Journal of Chemical Physics}, number = {2}, publisher = {American Institute of Physics}, title = {{An analytic model of rotationally inelastic collisions of polar molecules in electric fields}}, doi = {10.1063/1.2948392}, volume = {129}, year = {2008}, } @misc{2147, abstract = {We present the physics of the quantum Zeno effect, whose gist is often expressed by invoking the adage "a watched pot never boils". We review aspects of the theoretical and experimental work done on the effect since its inception in 1977, and mention some applications. We dedicate the article - with our very best wishes - to Rudolf Zahradnik at the occasion of his great jubilee. Perhaps Rudolf's lasting youthfulness and freshness are due to that he himself had been frequently observed throughout his life: until the political turn-around in 1989 by those who wished, by their surveillance, to prevent Rudolf from spoiling the youth by his personal culture and his passion for science and things beautiful and useful in general. This attempt had failed. Out of gratitude, the youth has infected Rudolf with its youthfulness. Chronically. Since 1989, Rudolf has been closely watched by the public at large. For the same traits of his as before, but with the opposite goal and for the benefit of all generations. We relish keeping him in sight...}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, booktitle = {Chemicke Listy}, number = {10}, pages = {880 -- 883}, publisher = {Czech Society of Chemical Engineering}, title = {{Kvantový Zenonův jev aneb co nesejde z očí, nezestárne}}, volume = {102}, year = {2008}, } @article{2148, abstract = {Despite the growing geological evidence that fluid boiling and vapour-liquid separation affect the distribution of metals in magmatic-hydrothermal systems significantly, there are few experimental data on the chemical status and partitioning of metals in the vapour and liquid phases. Here we report on an in situ measurement, using X-ray absorption fine structure (XAFS) spectroscopy, of antimony speciation and partitioning in the system Sb2O3-H2O-NaCl-HCl at 400°C and pressures 270–300 bar corresponding to the vapour-liquid equilibrium. Experiments were performed using a spectroscopic cell which allows simultaneous determination of the total concentration and atomic environment of the absorbing element (Sb) in each phase. Results show that quantitative vapour-brine separation of a supercritical aqueous salt fluid can be achieved by a controlled decompression and monitoring the X-ray absorbance of the fluid phase. Antimony concentrations in equilibrium with Sb2O3 (cubic, senarmontite) in the coexisting vapour and liquid phases and corresponding SbIII vapour-liquid partitioning coefficients are in agreement with recent data obtained using batch-reactor solubility techniques. The XAFS spectra analysis shows that hydroxy-chloride complexes, probably Sb(OH)2Cl0, are dominant both in the vapour and liquid phase in a salt-water system at acidic conditions. This first in situ XAFS study of element fractionation between coexisting volatile and dense phases opens new possibilities for systematic investigations of vapour-brine and fluid-melt immiscibility phenomena, avoiding many experimental artifacts common in less direct techniques.}, author = {Pokrovski, Gleb S and Roux, Jacques L and Hazemann, Jean L and Borisova, Anastassia Y and Gonchar, Anastasia A and Mikhail Lemeshko}, journal = {Mineralogical Magazine}, number = {2}, pages = {667 -- 681}, publisher = {Mineralogical Society}, title = {{In situ X-ray absorption spectroscopy measurement of vapour-brine fractionation of antimony at hydrothermal conditions}}, doi = {10.1180/minmag.2008.072.2.667 }, volume = {72}, year = {2008}, } @article{224, abstract = {Let n ≥ 4 and let Q ∈ [X1, ..., Xn] be a non-singular quadratic form. When Q is indefinite we provide new upper bounds for the least non-trivial integral solution to the equation Q = 0, and when Q is positive definite we provide improved upper bounds for the greatest positive integer k for which the equation Q = k is insoluble in integers, despite being soluble modulo every prime power.}, author = {Timothy Browning and Dietmann, Rainer}, journal = {Proceedings of the London Mathematical Society}, number = {2}, pages = {389 -- 416}, publisher = {John Wiley and Sons Ltd}, title = {{On the representation of integers by quadratic forms}}, doi = {10.1112/plms/pdm032}, volume = {96}, year = {2008}, } @article{225, abstract = {We revisit recent work of Heath-Brown on the average order of the quantity r(L1(x))⋯r(L4(x)), for suitable binary linear forms L1,...,L4, as x=(x1,x2) ranges over quite general regions in ℤ2. In addition to improving the error term in Heath-Browns estimate, we generalise his result to cover a wider class of linear forms.}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Compositio Mathematica}, number = {6}, pages = {1375 -- 1402}, publisher = {Cambridge University Press}, title = {{Binary linear forms as sums of two squares}}, doi = {10.1112/S0010437X08003692}, volume = {144}, year = {2008}, }