@article{8470,
  abstract     = {Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture).},
  author       = {Huber, Matthias and Hiller, Sebastian and Schanda, Paul and Ernst, Matthias and Böckmann, Anja and Verel, René and Meier, Beat H.},
  issn         = {1439-4235},
  journal      = {ChemPhysChem},
  keywords     = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics},
  number       = {5},
  pages        = {915--918},
  publisher    = {Wiley},
  title        = {{A proton-detected 4D solid-state NMR experiment for protein structure determination}},
  doi          = {10.1002/cphc.201100062},
  volume       = {12},
  year         = {2011},
}

@article{8471,
  abstract     = {Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general.},
  author       = {Van Melckebeke, Hélène and Schanda, Paul and Gath, Julia and Wasmer, Christian and Verel, René and Lange, Adam and Meier, Beat H. and Böckmann, Anja},
  issn         = {0022-2836},
  journal      = {Journal of Molecular Biology},
  number       = {3},
  pages        = {765--772},
  publisher    = {Elsevier},
  title        = {{Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR}},
  doi          = {10.1016/j.jmb.2010.11.004},
  volume       = {405},
  year         = {2011},
}

@article{8505,
  abstract     = {The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity.},
  author       = {Galante, Joseph and Kaloshin, Vadim},
  issn         = {0012-7094},
  journal      = {Duke Mathematical Journal},
  keywords     = {General Mathematics},
  number       = {2},
  pages        = {275--327},
  publisher    = {Duke University Press},
  title        = {{Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action}},
  doi          = {10.1215/00127094-1415878},
  volume       = {159},
  year         = {2011},
}

@inbook{881,
  author       = {Fyodor Kondrashov},
  booktitle    = {Evolution after Gene Duplication},
  pages        = {57 -- 76},
  publisher    = {Wiley-Blackwell},
  title        = {{Gene Dosage and Duplication}},
  doi          = {10.1002/9780470619902.ch4},
  year         = {2011},
}

@article{890,
  abstract     = {Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered.},
  author       = {Koblik, Evgeniy A and Red'Kin, Yaroslav A and Meer, Margarita S and Derelle, Romain and Golenkina, Sofia A and Fyodor Kondrashov and Arkhipov, Vladimir Y},
  journal      = {PLoS One},
  number       = {4},
  publisher    = {Public Library of Science},
  title        = {{Acrocephalus orinus: A case of Mistaken identity}},
  doi          = {10.1371/journal.pone.0017716},
  volume       = {6},
  year         = {2011},
}

@article{90,
  abstract     = {A popular method for generating micron-sized aerosols is to submerge ultrasonic (ω ∼ MHz) piezoelectric oscillators in a water bath. The submerged oscillator atomizes the fluid, creating droplets with radii proportional to the wavelength of the standing wave at the fluid surface. Classical theory for the Faraday instability predicts a parametric instability driving a capillary wave at the subharmonic (ω / 2) frequency. For many applications it is desirable to reduce the size of the droplets; however, using higher frequency oscillators becomes impractical beyond a few MHz. Observations are presented that demonstrate that smaller droplets may also be created by increasing the driving amplitude of the oscillator, and that this effect becomes more pronounced for large driving frequencies. It is shown that these observations are consistent with a transition from droplets associated with subharmonic (ω/2) capillary waves to harmonic (ω) capillary waves induced by larger driving frequencies and amplitudes, as predicted by a stability analysis of the capillary waves.},
  author       = {Higginbotham, Andrew P and Guillen, A and Jones, Nick and Donnelly, Tom and Bernoff, Andrew},
  journal      = {Journal of the Acoustical Society of America},
  number       = {5},
  pages        = {2694 -- 2699},
  publisher    = {Acoustical Society of America},
  title        = {{Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid}},
  doi          = {10.1121/1.3643816},
  volume       = {130},
  year         = {2011},
}

@article{1723,
  abstract     = {The emergence of differences in the arrangement of cells is the first step towards the establishment of many organs. Understanding this process is limited by the lack of systematic characterization of epithelial organisation. Here we apply network theory at the scale of individual cells to uncover patterns in cell-to-cell contacts that govern epithelial organisation. We provide an objective characterisation of epithelia using network representation, where cells are nodes and cell contacts are links. The features of individual cells, together with attributes of the cellular network, produce a defining signature that distinguishes epithelia from different organs, species, developmental stages and genetic conditions. The approach permits characterization, quantification and classification of normal and perturbed epithelia, and establishes a framework for understanding molecular mechanisms that underpin the architecture of complex tissues.},
  author       = {Escudero, Luis M and Costa, Luciano and Anna Kicheva and Briscoe, James and Freeman, Matthew and Babu, Madan M},
  journal      = {Nature Communications},
  number       = {1},
  publisher    = {Nature Publishing Group},
  title        = {{Epithelial organisation revealed by a network of cellular contacts}},
  doi          = {10.1038/ncomms1536},
  volume       = {2},
  year         = {2011},
}

@article{1724,
  abstract     = {Morphogens, such as Decapentaplegic (Dpp) in the fly imaginal discs, form graded concentration profiles that control patterning and growth of developing organs. In the imaginal discs, proliferative growth is homogeneous in space, posing the conundrum of how morphogen concentration gradients could control position-independent growth. To understand the mechanism of proliferation control by the Dpp gradient, we quantified Dpp concentration and signaling levels during wing disc growth. Both Dpp concentration and signaling gradients scale with tissue size during development. On average, cells divide when Dpp signaling levels have increased by 50%. Our observations are consistent with a growth control mechanism based on temporal changes of cellular morphogen signaling levels. For a scaling gradient, this mechanism generates position-independent growth rates.},
  author       = {Wartlick, Ortrud and Mumcu, Peer and Anna Kicheva and Bittig, Thomas and Seum, Carole and Jülicher, Frank and González-Gaitán, Marcos A},
  journal      = {Science},
  number       = {6021},
  pages        = {1154 -- 1159},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Dynamics of Dpp signaling and proliferation control}},
  doi          = {10.1126/science.1200037},
  volume       = {331},
  year         = {2011},
}

@article{1754,
  abstract     = {We report on a technique enabling electrical control of the contact silicidation process in silicon nanowire devices. Undoped silicon nanowires were contacted by pairs of nickel electrodes and each contact was selectively silicided by means of the Joule effect. By a realtime monitoring of the nanowire electrical resistance during the contact silicidation process we were able to fabricate nickel-silicide/silicon/nickel- silicide devices with controlled silicon channel length down to 8 nm. },
  author       = {Mongillo, Massimo and Spathis, Panayotis and Katsaros, Georgios and Gentile, Pascal and Sanquer, Marc and De Franceschi, Silvano},
  journal      = {ACS Nano},
  number       = {9},
  pages        = {7117 -- 7123},
  publisher    = {American Chemical Society},
  title        = {{Joule-assisted silicidation for short-channel silicon nanowire devices}},
  doi          = {10.1021/nn202524j},
  volume       = {5},
  year         = {2011},
}

@article{1755,
  abstract     = {Spin-selective tunneling of holes in SiGe nanocrystals contacted by normal-metal leads is reported. The spin selectivity arises from an interplay of the orbital effect of the magnetic field with the strong spin-orbit interaction present in the valence band of the semiconductor. We demonstrate both experimentally and theoretically that spin-selective tunneling in semiconductor nanostructures can be achieved without the use of ferromagnetic contacts. The reported effect, which relies on mixing the light and heavy holes, should be observable in a broad class of quantum-dot systems formed in semiconductors with a degenerate valence band.},
  author       = {Georgios Katsaros and Golovach, Vitaly N and Spathis, Panayotis N and Ares, Natalia and Stoffel, Mathieu and Fournel, Frank and Schmidt, Oliver G and Glazman, Leonid I and De Franceschi, Silvano},
  journal      = {Physical Review Letters},
  number       = {24},
  publisher    = {American Physical Society},
  title        = {{Observation of spin-selective tunneling in sige nanocrystals}},
  doi          = {10.1103/PhysRevLett.107.246601},
  volume       = {107},
  year         = {2011},
}

@article{1775,
  abstract     = {At optical frequencies the radiation produced by a source, such as a laser, a black body or a single-photon emitter, is frequently characterized by analysing the temporal correlations of emitted photons using single-photon counters. At microwave frequencies, however, there are no efficient single-photon counters yet. Instead, well-developed linear amplifiers allow for efficient measurement of the amplitude of an electromagnetic field. Here, we demonstrate first- and second-order correlation function measurements of a pulsed microwave-frequency single-photon source integrated on the same chip with a 50/50 beam splitter followed by linear amplifiers and quadrature amplitude detectors. We clearly observe single-photon coherence in first-order and photon antibunching in second-order correlation function measurements of the propagating fields.},
  author       = {Bozyigit, Deniz and Lang, C and Steffen, L. Kraig and Johannes Fink and Eichler, Christopher and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Filipp, Stefan and Da Silva, Marcus P and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Nature Physics},
  number       = {2},
  pages        = {154 -- 158},
  publisher    = {Nature Publishing Group},
  title        = {{Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors}},
  doi          = {10.1038/nphys1845},
  volume       = {7},
  year         = {2011},
}

@inproceedings{1776,
  abstract     = {Superconducting circuits have been successfully established as systems to prepare and investigate microwave light fields at the quantum level. In contrast to optical experiments where light is detected using photon counters, microwaves are usually measured with well developed linear amplifiers. This makes measurements of correlation functions - one of the important tools in optics - harder to achieve because they traditionally rely on photon counters and beam splitters. Here, we demonstrate a system where we can prepare on demand single microwave photons in a cavity and detect them at the two outputs of the cavity using linear amplifiers. Together with efficient data processing, this allows us to measure different observables of the cavity photons, including the first-order correlation function. Using these techniques we demonstrate cooling of a thermal background field in the cavity.},
  author       = {Bozyigit, Deniz and Lang, C and Steffen, L. Kraig and Johannes Fink and Eichler, Christopher and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Filipp, Stefan and Wallraff, Andreas and Da Silva, Marcus P and Blais, Alexandre},
  number       = {1},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Correlation measurements of individual microwave photons emitted from a symmetric cavity}},
  doi          = {10.1088/1742-6596/264/1/012024},
  volume       = {264},
  year         = {2011},
}

@article{1777,
  abstract     = {A wide range of experiments studying microwave photons localized in superconducting cavities have made important contributions to our understanding of the quantum properties of radiation. Propagating microwave photons, however, have so far been studied much less intensely. Here we present measurements in which we reconstruct the quantum state of itinerant single photon Fock states and their superposition with the vacuum by analyzing moments of the measured amplitude distribution up to fourth order. Using linear amplifiers and quadrature amplitude detectors, we have developed efficient methods to separate the detected single photon signal from the noise added by the amplifier. From our measurement data we have also reconstructed the corresponding Wigner function.},
  author       = {Eichler, Christopher and Bozyigit, Deniz and Lang, C and Steffen, L. and Fink, Johannes M and Wallraff, Andreas},
  journal      = {Physical Review Letters},
  number       = {22},
  publisher    = {American Physical Society},
  title        = {{Experimental state tomography of itinerant single microwave photons}},
  doi          = {10.1103/PhysRevLett.106.220503},
  volume       = {106},
  year         = {2011},
}

@article{1778,
  abstract     = {Creating a train of single photons and monitoring its propagation and interaction is challenging in most physical systems, as photons generally interact very weakly with other systems. However, when confining microwave frequency photons in a transmission line resonator, effective photon-photon interactions can be mediated by qubits embedded in the resonator. Here, we observe the phenomenon of photon blockade through second-order correlation function measurements. The experiments clearly demonstrate antibunching in a continuously pumped source of single microwave photons measured by using microwave beam splitters, linear amplifiers, and quadrature amplitude detectors. We also investigate resonance fluorescence and Rayleigh scattering in Mollow-triplet-like spectra.},
  author       = {Lang, C and Bozyigit, Deniz and Eichler, Christopher and Steffen, L. Kraig and Johannes Fink and Abdumalikov, Abdufarrukh A and Baur, Matthias P and Filipp, Stefan and Da Silva, Marcus P and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Physical Review Letters},
  number       = {24},
  publisher    = {American Physical Society},
  title        = {{Observation of resonant photon blockade at microwave frequencies using correlation function measurements}},
  doi          = {10.1103/PhysRevLett.106.243601},
  volume       = {106},
  year         = {2011},
}

@article{1780,
  abstract     = {Continuous variable entanglement between two modes of a radiation field is usually studied at optical frequencies. Here we demonstrate experiments that show the entanglement between microwave photons of different energy in a broadband squeezed beam. We use a Josephson parametric amplifier to generate the two-mode correlated state and detect all four quadrature components simultaneously in a two-channel heterodyne setup using amplitude detectors. Analyzing two-dimensional phase space histograms for all possible pairs of quadratures allows us to determine the full covariance matrix, which is in good agreement with the one expected for a two-mode squeezed state.},
  author       = {Eichler, Christopher and Bozyigit, Deniz and Lang, C and Baur, Matthias P and Steffen, L. Kraig and Johannes Fink and Filipp, Stefan and Wallraff, Andreas},
  journal      = {Physical Review Letters},
  number       = {11},
  publisher    = {American Physical Society},
  title        = {{Observation of two-mode squeezing in the microwave frequency domain}},
  doi          = {10.1103/PhysRevLett.107.113601},
  volume       = {107},
  year         = {2011},
}

@article{1781,
  abstract     = {Microwave cavities with high quality factors enable coherent coupling of distant quantum systems. Virtual photons lead to a transverse interaction between qubits when they are nonresonant with the cavity but resonant with each other. We experimentally investigate the inverse scaling of the interqubit coupling with the detuning from a cavity mode and its proportionality to the qubit-cavity interaction strength. We demonstrate that the enhanced coupling at higher frequencies is mediated by multiple higher-harmonic cavity modes. Moreover, we observe dark states of the coupled qubit-qubit system and analyze their relation to the symmetry of the applied driving field at different frequencies.},
  author       = {Filipp, Stefan and Göppl, M and Johannes Fink and Baur, Matthias P and Bianchetti, R and Steffen, L. Kraig and Wallraff, Andreas},
  journal      = {Physical Review A - Atomic, Molecular, and Optical Physics},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics}},
  doi          = {10.1103/PhysRevA.83.063827},
  volume       = {83},
  year         = {2011},
}

@article{1815,
  abstract     = {Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems.},
  author       = {Tamar Friedlander and Brenner, Naama},
  journal      = {Mathematical Biosciences and Engineering},
  number       = {2},
  pages        = {515 -- 526},
  publisher    = {Arizona State University},
  title        = {{Adaptive response and enlargement of dynamic range}},
  doi          = {10.3934/mbe.2011.8.515},
  volume       = {8},
  year         = {2011},
}

@article{1863,
  abstract     = {The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J>2, the proportion of parameter space affording this maximum is extremely small.},
  author       = {Sebastian Novak},
  journal      = {Theoretical Population Biology},
  number       = {3},
  pages        = {97 -- 101},
  publisher    = {Academic Press},
  title        = {{The number of equilibria in the diallelic Levene model with multiple demes}},
  doi          = {10.1016/j.tpb.2010.12.002},
  volume       = {79},
  year         = {2011},
}

@article{1973,
  abstract     = {Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.},
  author       = {Efremov, Rouslan G and Leonid Sazanov},
  journal      = {Nature},
  number       = {7361},
  pages        = {414 -- 421},
  publisher    = {Nature Publishing Group},
  title        = {{Structure of the membrane domain of respiratory complex i}},
  doi          = {10.1038/nature10330},
  volume       = {476},
  year         = {2011},
}

@article{1974,
  abstract     = {Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine.},
  author       = {Efremov, Rouslan G and Leonid Sazanov},
  journal      = {Current Opinion in Structural Biology},
  number       = {4},
  pages        = {532 -- 540},
  publisher    = {Elsevier},
  title        = {{Respiratory complex I: 'steam engine' of the cell?}},
  doi          = {10.1016/j.sbi.2011.07.002},
  volume       = {21},
  year         = {2011},
}