@misc{5428, abstract = {Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms. In this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan and Velner, Yaron}, issn = {2664-1690}, pages = {26}, publisher = {IST Austria}, title = {{Quantitative fair simulation games}}, doi = {10.15479/AT:IST-2014-315-v1-1}, year = {2014}, } @inproceedings{5810, abstract = {A discrete spherical geodesic path between two voxels s and t lying on a discrete sphere is a/the 1-connected shortest path from s to t, comprising voxels of the discrete sphere intersected by the real plane passing through s, t, and the center of the sphere. We show that the set of sphere voxels intersected by the aforesaid real plane always contains a 1-connected cycle passing through s and t, and each voxel in this set lies within an isothetic distance of 32 from the concerned plane. Hence, to compute the path, the algorithm starts from s, and iteratively computes each voxel p of the path from the predecessor of p. A novel number-theoretic property and the 48-symmetry of discrete sphere are used for searching the 1-connected voxels comprising the path. The algorithm is output-sensitive, having its time and space complexities both linear in the length of the path. It can be extended for constructing 1-connected discrete 3D circles of arbitrary orientations, specified by a few appropriate input parameters. Experimental results and related analysis demonstrate its efficiency and versatility.}, author = {Biswas, Ranita and Bhowmick, Partha}, isbn = {9783642387081}, issn = {0302-9743}, location = {Siena, Italy}, pages = {396--409}, publisher = {Springer}, title = {{On Finding Spherical Geodesic Paths and Circles in ℤ3}}, doi = {10.1007/978-3-319-09955-2_33}, volume = {8668}, year = {2014}, } @article{5813, abstract = {We consider homogeneous Bose gas in a large cubic box with periodic boundary conditions, at zero temperature. We analyze its excitation spectrum in a certain kind of a mean-field infinite-volume limit. We prove that under appropriate conditions the excitation spectrum has the form predicted by the Bogoliubov approximation. Our result can be viewed as an extension of the result of Seiringer (Commun. Math. Phys.306:565–578, 2011) to large volumes.}, author = {Dereziński, Jan and Napiórkowski, Marcin M}, issn = {1424-0637}, journal = {Annales Henri Poincaré}, number = {12}, pages = {2409--2439}, publisher = {Springer Nature}, title = {{Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit}}, doi = {10.1007/s00023-013-0302-4}, volume = {15}, year = {2014}, } @article{589, abstract = {We demonstrate a many-atom-cavity system with a high-finesse dual-wavelength standing wave cavity in which all participating rubidium atoms are nearly identically coupled to a 780-nm cavity mode. This homogeneous coupling is enforced by a one-dimensional optical lattice formed by the field of a 1560-nm cavity mode.}, author = {Lee, Jongmin and Vrijsen, Geert and Teper, Igor and Onur Hosten and Kasevich, Mark A}, journal = {Optics Letters}, number = {13}, pages = {4005 -- 4008}, publisher = {OSA}, title = {{Many-atom-cavity QED system with homogeneous atom-cavity coupling}}, doi = {10.1364/OL.39.004005}, volume = {39}, year = {2014}, } @article{6122, author = {Linneweber, Gerit A. and Jacobson, Jake and Busch, Karl Emanuel and Hudry, Bruno and Christov, Christo P. and Dormann, Dirk and Yuan, Michaela and Otani, Tomoki and Knust, Elisabeth and de Bono, Mario and Miguel-Aliaga, Irene}, issn = {0092-8674}, journal = {Cell}, number = {1-2}, pages = {69--83}, publisher = {Elsevier}, title = {{Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching}}, doi = {10.1016/j.cell.2013.12.008}, volume = {156}, year = {2014}, } @article{6124, abstract = {Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4 and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene encodes a conserved tail-anchored transmembrane protein; the molecular identity of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4 also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding, maturation, or export from the ER. The physical interaction between human ODR4 and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues required for protease activity can rescue all odr-8 mutant phenotypes tested. Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia, either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and Ufm1-independent functions in GPCR biogenesis.}, author = {Chen, Changchun and Itakura, Eisuke and Weber, Katherine P. and Hegde, Ramanujan S. and de Bono, Mario}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {3}, publisher = {Public Library of Science (PLoS)}, title = {{An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism}}, doi = {10.1371/journal.pgen.1004082}, volume = {10}, year = {2014}, } @article{6126, abstract = {Aerobic animals constantly monitor and adapt to changes in O2 levels. The molecular mechanisms involved in sensing O2 are, however, incompletely understood. Previous studies showed that a hexacoordinated globin called GLB-5 tunes the dynamic range of O2-sensing neurons in natural C. elegans isolates, but is defective in the N2 lab reference strain (McGrath et al., 2009; Persson et al., 2009). GLB-5 enables a sharp behavioral switch when O2 changes between 21 and 17%. Here, we show that GLB-5 also confers rapid behavioral and cellular recovery from exposure to hypoxia. Hypoxia reconfigures O2-evoked Ca2+ responses in the URX O2 sensors, and GLB-5 enables rapid recovery of these responses upon re-oxygenation. Forward genetic screens indicate that GLB-5's effects on O2 sensing require PDL-1, the C. elegans ortholog of mammalian PrBP/PDE6δ protein. In mammals, PDE6δ regulates the traffic and activity of prenylated proteins (Zhang et al., 2004; Norton et al., 2005). PDL-1 promotes localization of GCY-33 and GCY-35, atypical soluble guanylate cyclases that act as O2 sensors, to the dendritic endings of URX and BAG neurons, where they colocalize with GLB-5. Both GCY-33 and GCY-35 are predicted to be prenylated. Dendritic localization is not essential for GCY-35 to function as an O2 sensor, but disrupting pdl-1 alters the URX neuron's O2 response properties. Functional GLB-5 can restore dendritic localization of GCY-33 in pdl-1 mutants, suggesting GCY-33 and GLB-5 are in a complex. Our data suggest GLB-5 and the soluble guanylate cyclases operate in close proximity to sculpt O2 responses.}, author = {Gross, E. and Soltesz, Z. and Oda, S. and Zelmanovich, V. and Abergel, Z. and de Bono, Mario}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {50}, pages = {16726--16738}, publisher = {Society for Neuroscience}, title = {{GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings}}, doi = {10.1523/jneurosci.5368-13.2014}, volume = {34}, year = {2014}, } @inbook{6178, abstract = {Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.}, author = {Smutny, Michael and Behrndt, Martin and Campinho, Pedro and Ruprecht, Verena and Heisenberg, Carl-Philipp J}, booktitle = {Tissue Morphogenesis}, editor = {Nelson, Celeste}, isbn = {9781493911639}, issn = {1940-6029}, pages = {219--235}, publisher = {Springer}, title = {{UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo}}, doi = {10.1007/978-1-4939-1164-6_15}, volume = {1189}, year = {2014}, } @article{6319, abstract = {Nous étudions le comportement asymptotique du nombre de variétés dans une certaine classe ne satisfaisant pas le principe de Hasse. Cette étude repose sur des résultats récemmentobtenus par Colliot-Thélène.}, author = {Bretèche, Régis de la and Browning, Timothy D}, issn = {1246-7405}, journal = {Journal de Théorie des Nombres de Bordeaux}, number = {1}, pages = {25--44}, publisher = {Cellule MathDoc/CEDRAM}, title = {{Contre-exemples au principe de Hasse pour certains tores coflasques}}, doi = {10.5802/jtnb.857}, volume = {26}, year = {2014}, } @inproceedings{1507, abstract = {The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices.}, author = {Erdös, László}, booktitle = {Proceedings of the International Congress of Mathematicians}, location = {Seoul, Korea}, pages = {214 -- 236}, publisher = {International Congress of Mathematicians}, title = {{Random matrices, log-gases and Hölder regularity}}, volume = {3}, year = {2014}, } @inproceedings{1516, abstract = {We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero. }, author = {Bräunlich, Gerhard and Hainzl, Christian and Seiringer, Robert}, booktitle = {Proceedings of the QMath12 Conference}, location = {Berlin, Germany}, pages = {127 -- 137}, publisher = {World Scientific Publishing}, title = {{On the BCS gap equation for superfluid fermionic gases}}, doi = {10.1142/9789814618144_0007}, year = {2014}, } @article{1309, abstract = {We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation.}, author = {Julian Fischer}, journal = {Nonlinear Differential Equations and Applications}, number = {1}, pages = {27 -- 50}, publisher = {Birkhäuser}, title = {{Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models}}, doi = {10.1007/s00030-013-0235-0}, volume = {21}, year = {2014}, } @article{1312, abstract = {We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long.}, author = {Julian Fischer}, journal = {Archive for Rational Mechanics and Analysis}, number = {3}, pages = {771 -- 818}, publisher = {Springer}, title = {{Upper bounds on waiting times for the Thin-film equation: The case of weak slippage}}, doi = {10.1007/s00205-013-0690-0}, volume = {211}, year = {2014}, } @article{13399, abstract = {Nature has long inspired scientists with its seemingly unlimited ability to harness solar energy and to utilize it to drive various physiological processes. With the help of man-made molecular photoswitches, we now have the potential to outperform natural systems in many ways, with the ultimate goal of fabricating multifunctional materials that operate at different light wavelengths. An important challenge in developing light-controlled artificial molecular machines lies in attaining a detailed understanding of the photoisomerization-coupled conformational changes that occur in macromolecules and molecular assemblies. In this issue of ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting insights into the behavior of individual photoresponsive molecules and to identify contraction, extension, and crawling events accompanying light-induced isomerization.}, author = {Kundu, Pintu K. and Klajn, Rafal}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Physics and Astronomy, General Engineering, General Materials Science}, number = {12}, pages = {11913--11916}, publisher = {American Chemical Society}, title = {{Watching single molecules move in response to light}}, doi = {10.1021/nn506656r}, volume = {8}, year = {2014}, } @article{13400, abstract = {Organizing inorganic nanocrystals into complex architectures is challenging and typically relies on preexisting templates, such as properly folded DNA or polypeptide chains. We found that under carefully controlled conditions, cubic nanocrystals of magnetite self-assemble into arrays of helical superstructures in a template-free manner with >99% yield. Computer simulations revealed that the formation of helices is determined by the interplay of van der Waals and magnetic dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed to spontaneous formation of chiral nanocube clusters. Neighboring helices within their densely packed ensembles tended to adopt the same handedness in order to maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality amplification.}, author = {Singh, Gurvinder and Chan, Henry and Baskin, Artem and Gelman, Elijah and Repnin, Nikita and Král, Petr and Klajn, Rafal}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6201}, pages = {1149--1153}, publisher = {American Association for the Advancement of Science}, title = {{Self-assembly of magnetite nanocubes into helical superstructures}}, doi = {10.1126/science.1254132}, volume = {345}, year = {2014}, } @article{13401, abstract = {A compound combining the features of a molecular rotor and a photoswitch was synthesized and was shown to exist as three diastereomers, which interconvert via a reversible cyclic reaction scheme. Each of the three diastereomers was isolated, and by following the equilibration kinetics, activation barriers for all reactions were calculated. The results indicate that the properties of molecular switches depend heavily on their immediate chemical environment. The conclusions are important in the context of designing new switchable molecules and materials.}, author = {Kundu, Pintu K. and Lerner, Avishai and Kučanda, Kristina and Leitus, Gregory and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {32}, pages = {11276--11279}, publisher = {American Chemical Society}, title = {{Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran}}, doi = {10.1021/ja505948q}, volume = {136}, year = {2014}, } @article{13402, abstract = {Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation.}, author = {Kundu, Pintu K. and Olsen, Gregory L. and Kiss, Vladimir and Klajn, Rafal}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Nanoporous frameworks exhibiting multiple stimuli responsiveness}}, doi = {10.1038/ncomms4588}, volume = {5}, year = {2014}, } @article{13403, abstract = {We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles.}, author = {Zdobinsky, Tino and Sankar Maiti, Pradipta and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {7}, pages = {2711--2714}, publisher = {American Chemical Society}, title = {{Support curvature and conformational freedom control chemical reactivity of immobilized species}}, doi = {10.1021/ja411573a}, volume = {136}, year = {2014}, } @article{13404, abstract = {In the past few years, spiropyran has emerged as the molecule-of-choice for the construction of novel dynamic materials. This unique molecular switch undergoes structural isomerisation in response to a variety of orthogonal stimuli, e.g. light, temperature, metal ions, redox potential, and mechanical stress. Incorporation of this switch onto macromolecular supports or inorganic scaffolds allows for the creation of robust dynamic materials. This review discusses the synthesis, switching conditions, and use of dynamic materials in which spiropyran has been attached to the surfaces of polymers, biomacromolecules, inorganic nanoparticles, as well as solid surfaces. The resulting materials show fascinating properties whereby the state of the switch intimately affects a multitude of useful properties of the support. The utility of the spiropyran switch will undoubtedly endow these materials with far-reaching applications in the near future.}, author = {Klajn, Rafal}, issn = {1460-4744}, journal = {Chemical Society Reviews}, keywords = {General Chemistry}, number = {1}, pages = {148--184}, publisher = {Royal Society of Chemistry}, title = {{Spiropyran-based dynamic materials}}, doi = {10.1039/c3cs60181a}, volume = {43}, year = {2014}, } @article{1375, abstract = {We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound.}, author = {Chatterjee, Krishnendu and Henzinger, Monika H and Krinninger, Sebastian and Loitzenbauer, Veronika and Raskin, Michael}, journal = {Theoretical Computer Science}, number = {C}, pages = {104 -- 116}, publisher = {Elsevier}, title = {{Approximating the minimum cycle mean}}, doi = {10.1016/j.tcs.2014.06.031}, volume = {547}, year = {2014}, }