@misc{5421,
  abstract     = {Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are: (1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure). (2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.},
  author       = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Nowak, Martin},
  issn         = {2664-1690},
  pages        = {27},
  publisher    = {IST Austria},
  title        = {{The complexity of evolution on graphs}},
  doi          = {10.15479/AT:IST-2014-190-v2-2},
  year         = {2014},
}

@techreport{5422,
  abstract     = {Notes from the Third Plenary for the Research Data Alliance in Dublin, Ireland on March 26 to 28, 2014 with focus on starting an institutional research data repository.},
  author       = {Porsche, Jana},
  publisher    = {none},
  title        = {{Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland}},
  year         = {2014},
}

@misc{5423,
  abstract     = {We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm- deadline real-time tasks based on multi-objective graphs: Given a taskset and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. a clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including D(over), that have been proposed in the past, for various tasksets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are tasksets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application. },
  author       = {Chatterjee, Krishnendu and Kössler, Alexander and Pavlogiannis, Andreas and Schmid, Ulrich},
  issn         = {2664-1690},
  pages        = {14},
  publisher    = {IST Austria},
  title        = {{A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks}},
  doi          = {10.15479/AT:IST-2014-300-v1-1},
  year         = {2014},
}

@misc{5424,
  abstract     = {We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.},
  author       = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush},
  issn         = {2664-1690},
  pages        = {12},
  publisher    = {IST Austria},
  title        = {{Qualitative analysis of POMDPs with temporal logic specifications for robotics applications}},
  doi          = {10.15479/AT:IST-2014-305-v1-1},
  year         = {2014},
}

@misc{5425,
  abstract     = { We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objective we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest.},
  author       = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3 and Anonymous, 4},
  issn         = {2664-1690},
  pages        = {22},
  publisher    = {IST Austria},
  title        = {{Optimal cost almost-sure reachability in POMDPs}},
  year         = {2014},
}

@misc{5426,
  abstract     = {We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.},
  author       = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush},
  issn         = {2664-1690},
  pages        = {10},
  publisher    = {IST Austria},
  title        = {{Qualitative analysis of POMDPs with temporal logic specifications for robotics applications}},
  doi          = {10.15479/AT:IST-2014-305-v2-1},
  year         = {2014},
}

@misc{5427,
  abstract     = {We consider graphs with n nodes together with their tree-decomposition that has b = O ( n ) bags and width t , on the standard RAM computational model with wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution is an algorithm that given a graph and its tree-decomposition as input, computes a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph in O ( b ) time and space, improving a long-standing (from 1992) bound of O ( n · log n ) time for constant treewidth graphs. Our second contribution is on reachability queries for low treewidth graphs. We build on our tree-balancing algorithm and present a data-structure for graph reachability that requires O ( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time for pair queries, and O ( n · t · log t/ log n ) time for single-source queries. For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries.},
  author       = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
  issn         = {2664-1690},
  pages        = {24},
  publisher    = {IST Austria},
  title        = {{Optimal tree-decomposition balancing and reachability on low treewidth graphs}},
  doi          = {10.15479/AT:IST-2014-314-v1-1},
  year         = {2014},
}

@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},
}

@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},
}

@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{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{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},
}

@inproceedings{1392,
  abstract     = {Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption).},
  author       = {Dragoi, Cezara and Henzinger, Thomas A and Veith, Helmut and Widder, Josef and Zufferey, Damien},
  location     = {San Diego, USA},
  pages        = {161 -- 181},
  publisher    = {Springer},
  title        = {{A logic-based framework for verifying consensus algorithms}},
  doi          = {10.1007/978-3-642-54013-4_10},
  volume       = {8318},
  year         = {2014},
}