@article{1782, abstract = {Steering a quantum harmonic oscillator state along cyclic trajectories leads to a path-dependent geometric phase. Here we describe its experimental observation in an electronic harmonic oscillator. We use a superconducting qubit as a nonlinear probe of the phase, which is otherwise unobservable due to the linearity of the oscillator. We show that the geometric phase is, for a variety of cyclic paths, proportional to the area enclosed in the quadrature plane. At the transition to the nonadiabatic regime, we study corrections to the phase and dephasing of the qubit caused by qubit-resonator entanglement. In particular, we identify parameters for which this dephasing mechanism is negligible even in the nonadiabatic regime. The demonstrated controllability makes our system a versatile tool to study geometric phases in open quantum systems and to investigate their potential for quantum information processing.}, author = {Pechal, M and Berger, Stefan T and Abdumalikov, Abdufarrukh A and Johannes Fink and Mlynek, Jonas A and Steffen, L. Kraig and Wallraff, Andreas and Filipp, Stefan}, journal = {Physical Review Letters}, number = {17}, publisher = {American Physical Society}, title = {{Geometric phase and nonadiabatic effects in an electronic harmonic oscillator}}, doi = {10.1103/PhysRevLett.108.170401}, volume = {108}, year = {2012}, } @article{1783, abstract = {Nonlinearity and entanglement are two important properties by which physical systems can be identified as nonclassical. We study the dynamics of the resonant interaction of up to N=3 two-level systems and a single mode of the electromagnetic field sharing a single excitation dynamically. We observe coherent vacuum Rabi oscillations and their nonlinear √N speedup by tracking the populations of all qubits and the resonator in time. We use quantum state tomography to show explicitly that the dynamics generates maximally entangled states of the W class in a time limited only by the collective interaction rate. We use an entanglement witness and the 3-tangle to characterize the state whose fidelity F=78% is limited in our experiments by crosstalk arising during the simultaneous qubit manipulations which is absent in a sequential approach with F=91%.}, author = {Mlynek, Jonas A and Abdumalikov, Abdufarrukh A and Johannes Fink and Steffen, L. Kraig and Baur, Matthias P and Lang, C and Van Loo, Arjan F and Wallraff, Andreas}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {5}, publisher = {American Physical Society}, title = {{Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics}}, doi = {10.1103/PhysRevA.86.053838}, volume = {86}, year = {2012}, } @article{1784, abstract = {A localized qubit entangled with a propagating quantum field is well suited to study nonlocal aspects of quantum mechanics and may also provide a channel to communicate between spatially separated nodes in a quantum network. Here, we report the on-demand generation and characterization of Bell-type entangled states between a superconducting qubit and propagating microwave fields composed of zero-, one-, and two-photon Fock states. Using low noise linear amplification and efficient data acquisition we extract all relevant correlations between the qubit and the photon states and demonstrate entanglement with high fidelity.}, author = {Eichler, Christopher and Lang, C and Johannes Fink and Govenius, J and Filipp, Stefan and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {24}, publisher = {American Physical Society}, title = {{Observation of entanglement between itinerant microwave photons and a superconducting qubit}}, doi = {10.1103/PhysRevLett.109.240501}, volume = {109}, year = {2012}, } @article{1801, abstract = {Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of an individual adult brain region differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes in one brain region, the mouse retina. We found that each adult cell type expressed a specific set of genes, including a unique set of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes carried enough information to categorize cells into morphological classes and types. Several genes that were specifically expressed in particular retinal circuit elements, such as inhibitory neuron types, are associated with eye diseases. The resource described here allows gene expression to be compared across adult retinal cell types, experimenting with specific transcription factors to differentiate stem or somatic cells to retinal cell types, and predicting cellular targets of newly discovered disease-associated genes.}, author = {Sandra Siegert and Cabuy, Erik and Scherf, Brigitte G and Kohler, Hubertus and Panda, Satchidananda and Le, Yunzheng and Fehling, Hans J and Gaidatzis, Dimos and Stadler, Michael B and Roska, Botond M}, journal = {Nature Neuroscience}, number = {3}, pages = {487 -- 495}, publisher = {Nature Publishing Group}, title = {{Transcriptional code and disease map for adult retinal cell types}}, doi = {10.1038/nn.3032}, volume = {15}, year = {2012}, } @article{1972, abstract = {Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a "membrane lyzozyme" The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins.}, author = {Efremov, Rouslan G and Leonid Sazanov}, journal = {Journal of Structural Biology}, number = {3}, pages = {311 -- 318}, publisher = {Academic Press}, title = {{Structure of Escherichia coli OmpF porin from lipidic mesophase}}, doi = {10.1016/j.jsb.2012.03.005}, volume = {178}, year = {2012}, } @misc{1976, abstract = {Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes.}, author = {Efremov, Rouslan G and Leonid Sazanov}, booktitle = {Biochimica et Biophysica Acta - Bioenergetics}, number = {10}, pages = {1785 -- 1795}, publisher = {Elsevier}, title = {{The coupling mechanism of respiratory complex i - A structural and evolutionary perspective}}, doi = {10.1016/j.bbabio.2012.02.015}, volume = {1817}, year = {2012}, } @article{1987, abstract = {In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction-diffusion system. }, author = {Schweizer, Jakob and Martin Loose and Bonny, Mike and Kruse, Karsten and Mönch, Ingolf and Schwille, Petra }, journal = {PNAS}, number = {38}, pages = {15283 -- 15288}, publisher = {National Academy of Sciences}, title = {{Geometry sensing by self-organized protein patterns}}, doi = {10.1073/pnas.1206953109}, volume = {109}, year = {2012}, } @inproceedings{2048, abstract = {Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively.}, author = {Faust, Sebastian and Pietrzak, Krzysztof Z and Schipper, Joachim}, booktitle = { Conference proceedings CHES 2012}, location = {Leuven, Belgium}, pages = {213 -- 232}, publisher = {Springer}, title = {{Practical leakage-resilient symmetric cryptography}}, doi = {10.1007/978-3-642-33027-8_13}, volume = {7428}, year = {2012}, } @inproceedings{2049, abstract = {We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices. Performance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES. }, author = {Heyse, Stefan and Kiltz, Eike and Lyubashevsky, Vadim and Paar, Christof and Pietrzak, Krzysztof Z}, booktitle = { Conference proceedings FSE 2012}, location = {Washington, DC, USA}, pages = {346 -- 365}, publisher = {Springer}, title = {{Lapin: An efficient authentication protocol based on ring-LPN}}, doi = {10.1007/978-3-642-34047-5_20}, volume = {7549}, year = {2012}, } @article{13407, abstract = {We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light.}, author = {Chovnik, Olga and Balgley, Renata and Goldman, Joel R. and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {48}, pages = {19564--19567}, publisher = {American Chemical Society}, title = {{Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets}}, doi = {10.1021/ja309633v}, volume = {134}, year = {2012}, } @article{13408, abstract = {Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls.}, author = {Ridelman, Yonatan and Singh, Gurvinder and Popovitz-Biro, Ronit and Wolf, Sharon G. and Das, Sanjib and Klajn, Rafal}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {5}, pages = {654--660}, publisher = {Wiley}, title = {{Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles}}, doi = {10.1002/smll.201101882}, volume = {8}, year = {2012}, } @inproceedings{1384, abstract = {Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.}, author = {Beyer, Dirk and Henzinger, Thomas A and Keremoglu, Mehmet and Wendler, Philipp}, booktitle = {Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering}, location = {Cary, NC, USA}, publisher = {ACM}, title = {{Conditional model checking: A technique to pass information between verifiers}}, doi = {10.1145/2393596.2393664}, year = {2012}, } @article{1471, abstract = {Given a possibly reducible and non-reduced spectral cover π: X → C over a smooth projective complex curve C we determine the group of connected components of the Prym variety Prym(X/C). As an immediate application we show that the finite group of n-torsion points of the Jacobian of C acts trivially on the cohomology of the twisted SL n-Higgs moduli space up to the degree which is predicted by topological mirror symmetry. In particular this yields a new proof of a result of Harder-Narasimhan, showing that this finite group acts trivially on the cohomology of the twisted SL n stable bundle moduli space.}, author = {Tamas Hausel and Pauly, Christian}, journal = {Geometry and Topology}, number = {3}, pages = {1609 -- 1638}, publisher = {University of Warwick}, title = {{Prym varieties of spectral covers}}, doi = {10.2140/gt.2012.16.1609}, volume = {16}, year = {2012}, } @article{1472, abstract = {For G = GL 2, PGL 2, SL 2 we prove that the perverse filtration associated with the Hitchin map on the rational cohomology of the moduli space of twisted G-Higgs bundles on a compact Riemann surface C agrees with the weight filtration on the rational cohomology of the twisted G character variety of C when the cohomologies are identified via non-Abelian Hodge theory. The proof is accomplished by means of a study of the topology of the Hitchin map over the locus of integral spectral curves.}, author = {De Cataldo, Mark A and Tamas Hausel and Migliorini, Luca}, journal = {Annals of Mathematics}, number = {3}, pages = {1329 -- 1407}, publisher = {Princeton University Press}, title = {{Topology of hitchin systems and Hodge theory of character varieties: The case A 1}}, doi = {10.4007/annals.2012.175.3.7}, volume = {175}, year = {2012}, } @misc{5396, abstract = {We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can out-perform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.}, author = {Korc, Filip and Kolmogorov, Vladimir and Lampert, Christoph}, issn = {2664-1690}, pages = {13}, publisher = {IST Austria}, title = {{Approximating marginals using discrete energy minimization}}, doi = {10.15479/AT:IST-2012-0003}, year = {2012}, } @techreport{5398, abstract = {This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers.}, author = {Porsche, Jana}, publisher = {IST Austria}, title = {{Actual state of research data @ ISTAustria}}, year = {2012}, } @inbook{5745, author = {Gupta, Ashutosh}, booktitle = {Automated Technology for Verification and Analysis}, isbn = {9783642333859}, issn = {1611-3349}, location = {Thiruvananthapuram, Kerala, India}, pages = {107--121}, publisher = {Springer Berlin Heidelberg}, title = {{Improved Single Pass Algorithms for Resolution Proof Reduction}}, doi = {10.1007/978-3-642-33386-6_10}, volume = {7561}, year = {2012}, } @article{5839, abstract = {Canny's edge detection algorithm is a classical and robust method for edge detection in gray-scale images. The two significant features of this method are introduction of NMS (Non-Maximum Suppression) and double thresholding of the gradient image. Due to poor illumination, the region boundaries in an image may become vague, creating uncertainties in the gradient image. In this paper, we have proposed an algorithm based on the concept of type-2 fuzzy sets to handle uncertainties that automatically selects the threshold values needed to segment the gradient image using classical Canny’s edge detection algorithm. The results show that our algorithm works significantly well on different benchmark images as well as medical images (hand radiography images). }, author = {Biswas, Ranita and Sil, Jaya}, issn = {2212-0173}, journal = {Procedia Technology}, pages = {820--824}, publisher = {Elsevier}, title = {{An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets}}, doi = {10.1016/j.protcy.2012.05.134}, volume = {4}, year = {2012}, } @article{596, abstract = {The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation.}, author = {Bernecky, Carrie A and Taatjes, Dylan}, journal = {Journal of Molecular Biology}, number = {5}, pages = {387 -- 394}, publisher = {Elsevier}, title = {{Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly}}, doi = {10.1016/j.jmb.2012.02.014}, volume = {417}, year = {2012}, } @article{6136, abstract = {Tonic receptors convey stimulus duration and intensity and are implicated in homeostatic control. However, how tonic homeostatic signals are generated and how they reconfigure neural circuits and modify animal behavior is poorly understood. Here we show that Caenorhabditis elegans O2-sensing neurons are tonic receptors that continuously signal ambient [O2] to set the animal's behavioral state. Sustained signaling relied on a Ca2+ relay involving L-type voltage-gated Ca2+ channels, the ryanodine and the inositol-1,4,5-trisphosphate receptors. Tonic activity evoked continuous neuropeptide release, which helps elicit the enduring behavioral state associated with high [O2]. Sustained O2 receptor signaling was propagated to downstream neural circuits, including the hub interneuron RMG. O2 receptors evoked similar locomotory states at particular O2 concentrations, regardless of previous d[O2]/dt. However, a phasic component of the URX receptors' response to high d[O2]/dt, as well as tonic-to-phasic transformations in downstream interneurons, enabled transient reorientation movements shaped by d[O2]/dt. Our results highlight how tonic homeostatic signals can generate both transient and enduring behavioral change.}, author = {Busch, Karl Emanuel and Laurent, Patrick and Soltesz, Zoltan and Murphy, Robin Joseph and Faivre, Olivier and Hedwig, Berthold and Thomas, Martin and Smith, Heather L and de Bono, Mario}, issn = {1097-6256}, journal = {Nature Neuroscience}, number = {4}, pages = {581--591}, publisher = {Springer Nature}, title = {{Tonic signaling from O2 sensors sets neural circuit activity and behavioral state}}, doi = {10.1038/nn.3061}, volume = {15}, year = {2012}, }