@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{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}, } @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{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}, } @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{2073, abstract = {Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.}, author = {Zhou, Qi and Zhu, Hongmei and Huang, Quanfei and Zhao, Li and Zhang, Guo J and Roy, Scott W and Beatriz Vicoso and Xuan, Zhaolin and Ruan, Jue and Zhang, Yue and Zhao, Ruoping and Ye, Chen and Zhang, Xiuqing and Wang, Jùn and Wang, Wen and Bachtrog, Doris}, journal = {BMC Genomics}, number = {1}, publisher = {BioMed Central}, title = {{Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans}}, doi = {10.1186/1471-2164-13-109}, volume = {13}, year = {2012}, } @article{2079, abstract = {We introduce an algorithm and representation for fabricating 3D shape abstractions using mutually intersecting planar cut-outs. The planes have prefabricated slits at their intersections and are assembled by sliding them together. Often such abstractions are used as a sculptural art form or in architecture and are colloquially called ‘cardboard sculptures’. Based on an analysis of construction rules, we propose an extended binary space partitioning tree as an efficient representation of such cardboard models which allows us to quickly evaluate the feasibility of newly added planar elements. The complexity of insertion order quickly increases with the number of planar elements and manual analysis becomes intractable. We provide tools for generating cardboard sculptures with guaranteed constructibility. In combination with a simple optimization and sampling strategy for new elements, planar shape abstraction models can be designed by iteratively adding elements. As an output, we obtain a fabrication plan that can be printed or sent to a laser cutter. We demonstrate the complete process by designing and fabricating cardboard models of various well-known 3D shapes.}, author = {Hildebrand, Kristian and Bernd Bickel and Alexa, Marc}, journal = {Computer Graphics Forum}, number = {2pt3}, pages = {583 -- 592}, publisher = {Wiley-Blackwell}, title = {{crdbrd: Shape fabrication by sliding planar slices}}, doi = {10.1111/j.1467-8659.2012.03037.x}, volume = {31}, year = {2012}, } @article{2103, abstract = {Although facial hair plays an important role in individual expression, facial-hair reconstruction is not addressed by current facecapture systems. Our research addresses this limitation with an algorithm that treats hair and skin surface capture together in a coupled fashion so that a high-quality representation of hair fibers as well as the underlying skin surface can be reconstructed. We propose a passive, camera-based system that is robust against arbitrary motion since all data is acquired within the time period of a single exposure. Our reconstruction algorithm detects and traces hairs in the captured images and reconstructs them in 3D using a multiview stereo approach. Our coupled skin-reconstruction algorithm uses information about the detected hairs to deliver a skin surface that lies underneath all hairs irrespective of occlusions. In dense regions like eyebrows, we employ a hair-synthesis method to create hair fibers that plausibly match the image data. We demonstrate our scanning system on a number of individuals and show that it can successfully reconstruct a variety of facial-hair styles together with the underlying skin surface.}, author = {Beeler, Thabo and Bernd Bickel and Noris, Gioacchino and Beardsley, Paul A and Marschner, Steve and Sumner, Robert W and Groß, Markus S}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Coupled 3D reconstruction of sparse facial hair and skin}}, doi = {10.1145/2185520.2185613}, volume = {31}, year = {2012}, } @article{2101, abstract = {Articulated deformable characters are widespread in computer animation. Unfortunately, we lack methods for their automatic fabrication using modern additive manufacturing (AM) technologies. We propose a method that takes a skinned mesh as input, then estimates a fabricatable single-material model that approximates the 3D kinematics of the corresponding virtual articulated character in a piecewise linear manner. We first extract a set of potential joint locations. From this set, together with optional, user-specified range constraints, we then estimate mechanical friction joints that satisfy inter-joint non-penetration and other fabrication constraints. To avoid brittle joint designs, we place joint centers on an approximate medial axis representation of the input geometry, and maximize each joint's minimal cross-sectional area. We provide several demonstrations, manufactured as single, assembled pieces using 3D printers. }, author = {Bac̈her, Moritz and Bernd Bickel and James, Doug L and Pfister, Hanspeter}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Fabricating articulated characters from skinned meshes}}, doi = {10.1145/2185520.2185543}, volume = {31}, year = {2012}, } @article{2102, abstract = {We propose a complete process for designing, simulating, and fabricating synthetic skin for an animatronics character that mimics the face of a given subject and its expressions. The process starts with measuring the elastic properties of a material used to manufacture synthetic soft tissue. Given these measurements we use physicsbased simulation to predict the behavior of a face when it is driven by the underlying robotic actuation. Next, we capture 3D facial expressions for a given target subject. As the key component of our process, we present a novel optimization scheme that determines the shape of the synthetic skin as well as the actuation parameters that provide the best match to the target expressions. We demonstrate this computational skin design by physically cloning a real human face onto an animatronics figure. }, author = {Bernd Bickel and Kaufmann, Peter and Skouras, Mélina and Thomaszewski, Bernhard and Bradley, Derek J and Beeler, Thabo and Jackson, Philip V and Marschner, Steve and Matusik, Wojciech and Groß, Markus S}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Physical face cloning}}, doi = {10.1145/2185520.2185614}, volume = {31}, year = {2012}, } @inproceedings{2106, abstract = {Progress in cloth simulation for computer animation and apparel design has led to a multitude of deformation models, each with its own way of relating geometry, deformation, and forces. As simulators improve, differences between these models become more important, but it is difficult to choose a model and a set of parameters to match a given real material simply by looking at simulation results. This paper provides measurement and fitting methods that allow nonlinear models to be fit to the observed deformation of a particular cloth sample. Unlike standard textile testing, our system measures complex 3D deformations of a sheet of cloth, not just one-dimensional force-displacement curves, so it works under a wider range of deformation conditions. The fitted models are then evaluated by comparison to measured deformations with motions very different from those used for fitting.}, author = {Miguel, Eder and Bradley, Derek J and Thomaszewski, Bernhard and Bernd Bickel and Matusik, Wojciech and Otaduy, Miguel A and Marschner, Steve}, number = {2}, pages = {519 -- 528}, publisher = {Wiley-Blackwell}, title = {{Data-driven estimation of cloth simulation models}}, doi = {10.1111/j.1467-8659.2012.03031.x}, volume = {31}, year = {2012}, } @inproceedings{2104, abstract = {In recent years, various methods have been introduced to exploit pre-recorded data to improve the performance and/or realism of dynamic deformations, but their differences and similarities have not been adequately analyzed or discussed. So far, the proposed methods have been explored mainly in the research context. They have not been adopted by the computer graphics industry. This course bridges the gap between research labs and industry to present a unifying theory and understanding of data-driven methods for dynamic deformations that may inspire development of novel solutions. It focuses on application of data-driven methods to three areas of computer animation: dynamic deformation of faces, soft volumetric tissue, and cloth. And it describes how to approach these challenges in a data-driven manner, classifies the various methods, and demonstrates how data-driven methods can work in other settings. }, author = {Otaduy, Miguel A and Bernd Bickel and Bradley, Derek J and Wang, Huamin}, publisher = {ACM}, title = {{Data-driven simulation methods in computer graphics: Cloth, tissue and faces}}, doi = {10.1145/2343483.2343495}, year = {2012}, } @inproceedings{2105, author = {Skouras, Mélina and Thomaszewski, Bernhard and Bernd Bickel and Groß, Markus S}, number = {2}, pages = {835 -- 844}, publisher = {Wiley-Blackwell}, title = {{Computational design of rubber balloons}}, doi = {10.1111/j.1467-8659.2012.03064.x}, volume = {31}, year = {2012}, } @article{2125, abstract = {We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs.}, author = {Hairer, Martin M and Jan Maas}, journal = {Annals of Probability}, number = {4}, pages = {1675 -- 1714}, publisher = {Institute of Mathematical Statistics}, title = {{A spatial version of the Itô-Stratonovich correction}}, doi = {10.1214/11-AOP662}, volume = {40}, year = {2012}, } @article{2127, abstract = {We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube.}, author = {Erbar, Matthias and Jan Maas}, journal = {Archive for Rational Mechanics and Analysis}, number = {3}, pages = {997 -- 1038}, publisher = {Springer}, title = {{Ricci curvature of finite Markov chains via convexity of the entropy}}, doi = {10.1007/s00205-012-0554-z}, volume = {206}, year = {2012}, } @article{2128, abstract = {We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein.}, author = {Jan Maas and van Neerven, Jan M and Portal, Pierre}, journal = {Arkiv för Matematik}, number = {2}, pages = {379 -- 395}, publisher = {Springer}, title = {{Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure}}, doi = {10.1007/s11512-010-0143-z}, volume = {50}, year = {2012}, } @article{2203, abstract = {We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off-resonant optical field. The combined interaction potential becomes tunable by variation of wavelength, polarisation and intensity of the optical field and its dependence on the intermolecular separation exhibits a crossover from an inverse-power to an oscillating behaviour. The ability thereby offered to control molecular interactions opens up avenues toward the creation and manipulation of novel phases of ultracold polar gases among whose characteristics is a long-range entanglement of the dipoles' mutual orientation. We devised an accurate analytic model of such optical-field-dressed dipole-dipole interaction potentials, which enables a straightforward access to the optical-field parameters required for the design of intermolecular interactions in the laboratory.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Molecular Physics}, number = {15-16}, pages = {1873 -- 1881}, publisher = {Taylor & Francis}, title = {{Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other}}, doi = {10.1080/00268976.2012.689868}, volume = {110}, year = {2012}, } @article{2201, abstract = {We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation.}, author = {Lemeshko, Mikhail and Krems, Roman and Weimer, Hendrik}, journal = {Physical Review Letters}, number = {3}, publisher = {American Physical Society}, title = {{Nonadiabatic preparation of spin crystals with ultracold polar molecules}}, doi = {10.1103/PhysRevLett.109.035301}, volume = {109}, year = {2012}, } @article{2202, abstract = {We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime.}, author = {Alyabyshev, Sergey V and Mikhail Lemeshko and Krems, Roman V}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {1}, publisher = {American Physical Society}, title = {{Sensitive imaging of electromagnetic fields with paramagnetic polar molecules}}, doi = {10.1103/PhysRevA.86.013409}, volume = {86}, year = {2012}, } @article{2263, abstract = {Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.}, author = {Liang, Huixuan and Hippenmeyer, Simon and Ghashghaei, H.}, journal = {Biology open}, number = {12}, pages = {1200 -- 1203}, publisher = {The Company of Biologists}, title = {{A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors}}, doi = {10.1242/bio.20122287}, volume = {1}, year = {2012}, } @inproceedings{2267, abstract = {Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications. }, author = {Preiner, Reinhold and Jeschke, Stefan and Wimmer, Michael}, location = {Calgari, Italy}, pages = {139 -- 148}, publisher = {Eurographics Association}, title = {{Auto splats: Dynamic point cloud visualization on the GPU}}, doi = {10.2312/EGPGV/EGPGV12/139-148}, year = {2012}, } @article{2262, abstract = {Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM.}, author = {Tasic, Bosiljka and Miyamichi, Kazunari and Simon Hippenmeyer and Dani, Vardhan S. and Zeng, H. and Joo, William and Zong, Hui and Chen-Tsai, Yanru and Luo, Liqun}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Extensions of MADM (Mosaic Analysis with Double Markers) in Mice }}, doi = {10.1371/journal.pone.0033332}, volume = {7}, year = {2012}, } @inproceedings{2268, abstract = {This paper presents an analytic formulation for anti-aliased sampling of 2D polygons and 3D polyhedra. Our framework allows the exact evaluation of the convolution integral with a linear function defined on the polytopes. The filter is a spherically symmetric polynomial of any order, supporting approximations to refined variants such as the Mitchell-Netravali filter family. This enables high-quality rasterization of triangles and tetrahedra with linearly interpolated vertex values to regular and non-regular grids. A closed form solution of the convolution is presented and an efficient implementation on the GPU using DirectX and CUDA C is described. }, author = {Thomas Auzinger and Guthe, Michael and Stefan Jeschke}, number = {121}, pages = {335 -- 344}, publisher = {Wiley-Blackwell}, title = {{Analytic anti-aliasing of linear functions on polytopes}}, doi = {http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x}, volume = {31}, year = {2012}, } @article{2302, abstract = {We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.}, author = {Henzinger, Thomas A and Mateescu, Maria}, journal = {IEEE ACM Transactions on Computational Biology and Bioinformatics}, number = {2}, pages = {310 -- 322}, publisher = {IEEE}, title = {{The propagation approach for computing biochemical reaction networks}}, doi = {10.1109/TCBB.2012.91}, volume = {10}, year = {2012}, } @article{2313, abstract = {The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders.}, author = {Dixon-Salazar, Tracy J and Silhavy, Jennifer L and Udpa, Nitin and Schroth, Jana and Bielas, Stephanie L and Schaffer, Ashleigh E and Olvera, Jesus and Bafna, Vineet K and Zaki, Maha S and Abdel-Salam, Ghada M and Mansour, Lobna A and Selim, Laila A and Abdel-Hadi, Sawsan S and Marzouki, Naima and Ben-Omran, Tawfeg I and Al-Saana, Nouriya A and Sönmez, Fatma M and Celep, Figen and Azam, Matloob and Hill, Kiley J and Collazo, Adrienne and Fenstermaker, Ali G and Gaia Novarino and Akizu, Naiara and Garimella, Kiran V and Sougnez, Carrie L and Russ, Carsten and Gabriel, Stacey B and Gleeson, Joseph G}, journal = {Science Translational Medicine}, number = {138}, publisher = {American Association for the Advancement of Science}, title = {{Exome sequencing can improve diagnosis and alter patient management}}, doi = {10.1126/scitranslmed.3003544}, volume = {4}, year = {2012}, } @article{2314, abstract = {Autism spectrum disorders are a genetically heterogeneous constellation of syndromes characterized by impairments in reciprocal social interaction. Available somatic treatments have limited efficacy. We have identified inactivating mutations in the gene BCKDK (Branched Chain Ketoacid Dehydrogenase Kinase) in consanguineous families with autism, epilepsy, and intellectual disability. The encoded protein is responsible for phosphorylation-mediated inactivation of the E1α subunit of branched-chain ketoacid dehydrogenase (BCKDH). Patients with homozygous BCKDK mutations display reductions in BCKDK messenger RNA and protein, E1α phosphorylation, and plasma branched-chain amino acids. Bckdk knockout mice show abnormal brain amino acid profiles and neurobehavioral deficits that respond to dietary supplementation. Thus, autism presenting with intellectual disability and epilepsy caused by BCKDK mutations represents a potentially treatable syndrome.}, author = {Gaia Novarino and El-Fishawy, Paul and Kayserili, Hülya and Meguid, Nagwa A and Scott, Eric M and Schroth, Jana and Silhavy, Jennifer L and Kara, Majdi and Khalil, Rehab O and Ben-Omran, Tawfeg I and Ercan-Sencicek, Adife G and Hashish, Adel F and Sanders, Stephan J and Gupta, Abha R and Hashem, Hebatalla S and Matern, Dietrich and Gabriel, Stacey B and Sweetman, Lawrence and Rahimi, Yasmeen and Harris, Robert A and State, Matthew W and Gleeson, Joseph G}, journal = {Science}, number = {6105}, pages = {394 -- 397}, publisher = {American Association for the Advancement of Science}, title = {{Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy}}, doi = {10.1126/science.1224631}, volume = {338}, year = {2012}, } @article{2318, abstract = {We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential. }, author = {Seiringer, Robert}, journal = {Journal of Spectral Theory}, number = {3}, pages = {321--328}, publisher = {European Mathematical Society}, title = {{Absence of bound states implies non-negativity of the scattering length}}, doi = {10.4171/JST/31}, volume = {2}, year = {2012}, } @inproceedings{2317, abstract = {We present a summary of our recent rigorous derivation of the celebrated Ginzburg-Landau (GL) theory, starting from the microscopic Bardeen-Cooper-Schrieffer (BCS) model. Close to the critical temperature, GL arises as an effective theory on the macroscopic scale. The relevant scaling limit is semiclassical in nature, and semiclassical analysis, with minimal regularity assumptions, plays an important part in our proof. }, author = {Frank, Rupert L and Hainzl, Christian and Robert Seiringer and Solovej, Jan P}, pages = {575 -- 583}, publisher = {World Scientific Publishing}, title = {{Microscopic derivation of the Ginzburg-Landau model}}, doi = {10.1142/9789814449243_0060}, year = {2012}, } @inproceedings{2316, abstract = {We summarize our recent results on the ground state energy of multi-polaron systems. In particular, we discuss stability and existence of the thermodynamic limit, and we discuss the absence of binding in the case of large Coulomb repulsion and the corresponding binding-unbinding transition. We also consider the Pekar-Tomasevich approximation to the ground state energy and we study radial symmetry of the ground state density. }, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer and Thomas, Lawrence E}, pages = {477 -- 485}, publisher = {World Scientific Publishing}, title = {{Ground state properties of multi-polaron systems}}, doi = {10.1142/9789814449243_0045}, year = {2012}, } @article{237, abstract = {The Manin conjecture is established for Châtelet surfaces over Q aris-ing as minimal proper smooth models of the surface Y 2 + Z 2 = f(X) in A 3 Q, where f ∈ Z[X] is a totally reducible polynomial of degree 3 without repeated roots. These surfaces do not satisfy weak approximation.}, author = {de la Bretèche, Régis and Timothy Browning and Peyre, Emmanuel}, journal = {Annals of Mathematics}, number = {1}, pages = {297 -- 343}, publisher = {Princeton University Press}, title = {{On Manin's conjecture for a family of Châtelet surfaces}}, doi = {10.4007/annals.2012.175.1.8}, volume = {175}, year = {2012}, } @article{238, abstract = {For given positive integers a, b, q we investigate the density of solutions (x, y) ∈ Z2 to congruences ax + by2 ≡ 0 mod q.}, author = {Baier, Stephan and Timothy Browning}, journal = {Functiones et Approximatio, Commentarii Mathematici}, number = {2}, pages = {267 -- 286}, publisher = {Adam Mickiewicz University Press}, title = {{Inhomogeneous quadratic congruences}}, doi = {10.7169/facm/2012.47.2.9}, volume = {47}, year = {2012}, } @inbook{2399, abstract = {Bose–Einstein condensation (BEC) in cold atomic gases was first achieved experimentally in 1995 [1, 6]. After initial failed attempts with spin-polarized atomic hydrogen, the first successful demonstrations of this phenomenon used gases of rubidium and sodium atoms, respectively. Since then there has been a surge of activity in this field, with ingenious experiments putting forth more and more astonishing results about the behavior of matter at very cold temperatures. }, author = {Robert Seiringer}, booktitle = {Quantum Many Body Systems}, editor = {Rivasseau, Vincent and Robert Seiringer and Solovej, Jan P and Spencer, Thomas}, pages = {55 -- 92}, publisher = {Springer}, title = {{Cold quantum gases and bose einstein condensation}}, doi = {10.1007/978-3-642-29511-9_2}, volume = {2051}, year = {2012}, } @article{2394, abstract = {We study the BCS gap equation for a Fermi gas with unequal population of spin-up and spin-down states. For cosh (δ μ/T) ≤ 2, with T the temperature and δμ the chemical potential difference, the question of existence of non-trivial solutions can be reduced to spectral properties of a linear operator, similar to the unpolarized case studied previously in [Frank, R. L., Hainzl, C., Naboko, S., and Seiringer, R., J., Geom. Anal.17, 559-567 (2007)10.1007/BF02937429; Hainzl, C., Hamza, E., Seiringer, R., and Solovej, J. P., Commun., Math. Phys.281, 349-367 (2008)10.1007/s00220-008-0489-2; and Hainzl, C. and Seiringer, R., Phys. Rev. B77, 184517-110 435 (2008)]10.1103/PhysRevB.77.184517. For cosh (δ μ/T) > 2 the phase diagram is more complicated, however. We derive upper and lower bounds for the critical temperature, and study their behavior in the small coupling limit.}, author = {Freiji, Abraham and Hainzl, Christian and Robert Seiringer}, journal = {Journal of Mathematical Physics}, number = {1}, publisher = {American Institute of Physics}, title = {{The gap equation for spin-polarized fermions}}, doi = {10.1063/1.3670747}, volume = {53}, year = {2012}, } @article{2395, abstract = {We give the first rigorous derivation of the celebrated Ginzburg-Landau (GL) theory, starting from the microscopic Bardeen-Cooper-Schrieffer (BCS) model. Close to the critical temperature, GL arises as an effective theory on the macroscopic scale. The relevant scaling limit is semiclassical in nature, and semiclassical analysis, with minimal regularity assumptions, plays an important part in our proof. }, author = {Frank, Rupert L and Hainzl, Christian and Robert Seiringer and Solovej, Jan P}, journal = {Journal of the American Mathematical Society}, number = {3}, pages = {667 -- 713}, publisher = {American Mathematical Society}, title = {{Microscopic derivation of Ginzburg-Landau theory}}, doi = {10.1090/S0894-0347-2012-00735-8}, volume = {25}, year = {2012}, } @article{2396, abstract = {A positive temperature analogue of the scattering length of a potential V can be defined via integrating the difference of the heat kernels of -Δ and, with Δ the Laplacian. An upper bound on this quantity is a crucial input in the derivation of a bound on the critical temperature of a dilute Bose gas (Seiringer and Ueltschi in Phys Rev B 80:014502, 2009). In (Seiringer and Ueltschi in Phys Rev B 80:014502, 2009), a bound was given in the case of finite range potentials and sufficiently low temperature. In this paper, we improve the bound and extend it to potentials of infinite range.}, author = {Landon, Benjamin and Robert Seiringer}, journal = {Letters in Mathematical Physics}, number = {3}, pages = {237 -- 243}, publisher = {Springer}, title = {{The scattering length at positive temperature}}, doi = {10.1007/s11005-012-0566-5}, volume = {100}, year = {2012}, } @misc{2398, abstract = {We extend the mathematical theory of quantum hypothesis testing to the general W*-algebraic setting and explore its relation with recent developments in non-equilibrium quantum statistical mechanics. In particular, we relate the large deviation principle for the full counting statistics of entropy flow to quantum hypothesis testing of the arrow of time.}, author = {Jakšić, Vojkan and Ogata, Yoshiko and Pillet, Claude A and Robert Seiringer}, booktitle = {Reviews in Mathematical Physics}, number = {6}, publisher = {World Scientific Publishing}, title = {{Quantum hypothesis testing and non-equilibrium statistical mechanics}}, doi = {10.1142/S0129055X12300026}, volume = {24}, year = {2012}, } @article{2397, abstract = {We consider the low-density limit of a Fermi gas in the BCS approximation. We show that if the interaction potential allows for a two-particle bound state, the system at zero temperature is well approximated by the Gross-Pitaevskii functional, describing a Bose-Einstein condensate of fermion pairs.}, author = {Hainzl, Christian and Robert Seiringer}, journal = {Letters in Mathematical Physics}, number = {2}, pages = {119 -- 138}, publisher = {Springer}, title = {{Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs}}, doi = {10.1007/s11005-011-0535-4}, volume = {100}, year = {2012}, } @article{240, abstract = {We investigate the frequency of positive squareful numbers x, y, z≤B for which x+y=z and present a conjecture concerning its asymptotic behavior.}, author = {Timothy Browning and Valckenborgh, K Van}, journal = {Experimental Mathematics}, number = {2}, pages = {204 -- 211}, publisher = {Taylor & Francis}, title = {{Sums of three squareful numbers}}, doi = {10.1080/10586458.2011.605733}, volume = {21}, year = {2012}, } @article{2400, abstract = {If the polaron coupling constant α is large enough, bipolarons or multi-polarons will form. When passing through the critical α c from above, does the radius of the system simply get arbitrarily large or does it reach a maximum and then explode? We prove that it is always the latter. We also prove the analogous statement for the Pekar-Tomasevich (PT) approximation to the energy, in which case there is a solution to the PT equation at α c. Similarly, we show that the same phenomenon occurs for atoms, e. g., helium, at the critical value of the nuclear charge. Our proofs rely only on energy estimates, not on a detailed analysis of the Schrödinger equation, and are very general. They use the fact that the Coulomb repulsion decays like 1/r, while 'uncertainty principle' localization energies decay more rapidly, as 1/r 2.}, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {405 -- 424}, publisher = {Springer}, title = {{Binding of polarons and atoms at threshold}}, doi = {10.1007/s00220-012-1436-9}, volume = {313}, year = {2012}, } @article{2403, abstract = {We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose-Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wavefunction of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers and strong interactions the wavefunction extends over the whole interval. A high density of scatterers and weak interactions, on the other hand, lead to localization of the wavefunction in a fragmented subset of the interval.}, author = {Robert Seiringer and Yngvason, Jakob and Zagrebnov, Valentin A}, journal = {Journal of Statistical Mechanics Theory and Experiment}, number = {11}, publisher = {IOP Publishing Ltd.}, title = {{Disordered Bose-Einstein condensates with interaction in one dimension}}, doi = {10.1088/1742-5468/2012/11/P11007}, volume = {2012}, year = {2012}, } @article{2402, abstract = {We consider a model of quantum-mechanical particles interacting via point interactions of infinite scattering length. In the case of fermions we prove a Lieb-Thirring inequality for the energy, i.e., we show that the energy is bounded from below by a constant times the integral of the particle density to the power.}, author = {Frank, Rupert L and Robert Seiringer}, journal = {Journal of Mathematical Physics}, number = {9}, publisher = {American Institute of Physics}, title = {{Lieb-Thirring inequality for a model of particles with point interactions}}, doi = {10.1063/1.3697416}, volume = {53}, year = {2012}, } @article{2401, abstract = {We find further implications of the BMV conjecture, which states that for hermitian matrices B≥0 and A, the function λ {mapping} Tr exp(A - λB) is the Laplace transform of a positive measure supported on [0,∞].}, author = {Lieb, Élliott H and Robert Seiringer}, journal = {Journal of Statistical Physics}, number = {1}, pages = {86 -- 91}, publisher = {Springer}, title = {{Further implications of the Bessis-Moussa-Villani conjecture}}, doi = {10.1007/s10955-012-0585-8}, volume = {149}, year = {2012}, } @article{2411, abstract = {The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.}, author = {Ebersberger, Ingo and De Matos Simoes, Ricardo and Kupczok, Anne and Gube, Matthias and Kothe, Erika and Voigt, Kerstin and Von Haeseler, Arndt}, journal = {Molecular Biology and Evolution}, number = {5}, pages = {1319 -- 1334}, publisher = {Oxford University Press}, title = {{A consistent phylogenetic backbone for the fungi}}, doi = {10.1093/molbev/msr285}, volume = {29}, year = {2012}, } @article{241, abstract = {The representation of integral binary forms as sums of two squares is discussed and applied to establish the Manin conjecture for certain Châtelet surfaces over ℚ.}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Israel Journal of Mathematics}, number = {2}, pages = {973 -- 1012}, publisher = {Springer}, title = {{Binary forms as sums of two squares and Châtelet surfaces}}, doi = {10.1007/s11856-012-0019-y}, volume = {191}, year = {2012}, } @article{242, abstract = {We investigate the first and second moments of shifted convolutions of the generalized divisor function d 3(n).}, author = {Baier, Stephan and Timothy Browning and Marasingha, Gihan and Zhao, Liangyi}, journal = {Proceedings of the Edinburgh Mathematical Society}, number = {3}, pages = {551 -- 576}, publisher = {Cambridge University Press}, title = {{Averages of shifted convolutions of d3 (n)}}, doi = {10.1017/S001309151100037X}, volume = {55}, year = {2012}, } @article{243, abstract = {Let P(t) ∈ ℚ[t] be an irreducible quadratic polynomial and suppose that K is a quartic extension of ℚ containing the roots of P(t). Let N K/ℚ(X) be a full norm form for the extension K/ℚ. We show that the variety P(t) =N K/ℚ(X)≠ 0 satisfies the Hasse principle and weak approximation. The proof uses analytic methods.}, author = {Timothy Browning and Heath-Brown, Roger}, journal = {Geometric and Functional Analysis}, number = {5}, pages = {1124 -- 1190}, publisher = {Springer Basel}, title = {{Quadratic polynomials represented by norm forms}}, doi = {10.1007/s00039-012-0168-5}, volume = {22}, year = {2012}, } @inproceedings{2440, abstract = {We present an algorithm for computing [X, Y], i.e., all homotopy classes of continuous maps X → Y, where X, Y are topological spaces given as finite simplicial complexes, Y is (d - 1)-connected for some d ≥ 2 (for example, Y can be the d-dimensional sphere S d), and dim X ≤ 2d - 2. These conditions on X, Y guarantee that [X, Y] has a natural structure of a finitely generated Abelian group, and the algorithm finds generators and relations for it. We combine several tools and ideas from homotopy theory (such as Postnikov systems, simplicial sets, and obstruction theory) with algorithmic tools from effective algebraic topology (objects with effective homology). We hope that a further extension of the methods developed here will yield an algorithm for computing, in some cases of interest, the ℤ 2-index, which is a quantity playing a prominent role in Borsuk-Ulam style applications of topology in combinatorics and geometry, e.g., in topological lower bounds for the chromatic number of a graph. In a certain range of dimensions, deciding the embeddability of a simplicial complex into ℝ d also amounts to a ℤ 2-index computation. This is the main motivation of our work. We believe that investigating the computational complexity of questions in homotopy theory and similar areas presents a fascinating research area, and we hope that our work may help bridge the cultural gap between algebraic topology and theoretical computer science.}, author = {Čadek, Martin and Marek Krcál and Matoušek, Jiří and Sergeraert, Francis and Vokřínek, Lukáš and Uli Wagner}, pages = {1 -- 10}, publisher = {SIAM}, title = {{Computing all maps into a sphere}}, year = {2012}, }