@article{252,
abstract = {For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k.},
author = {Timothy Browning and Jones, Michael S},
journal = {Acta Arithmetica},
number = {3},
pages = {271 -- 298},
publisher = {Instytut Matematyczny},
title = {{Counting rational points on del Pezzo surfaces with a conic bundle structure}},
doi = {10.4064/aa163-3-6},
volume = {163},
year = {2014},
}
@article{254,
abstract = {A new "polynomial sieve" is presented and used to show that almost all integers have at most one representation as a sum of two values of a given polynomial of degree at least 3.},
author = {Timothy Browning},
journal = {International Mathematics Research Notices},
number = {7},
pages = {1987 -- 2019},
publisher = {Oxford University Press},
title = {{The polynomial sieve and equal sums of like polynomials}},
doi = {10.1093/imrn/rnt350},
volume = {2015},
year = {2014},
}
@article{255,
abstract = {We investigate the Hasse principle for complete intersections cut out by a quadric hypersurface and a cubic hypersurface defined over the rational numbers.},
author = {Timothy Browning and Dietmann, Rainer and Heath-Brown, Roger},
journal = {Journal of the Institute of Mathematics of Jussieu},
number = {4},
pages = {703 -- 749},
publisher = {Cambridge University Press},
title = {{Rational points on intersections of cubic and quadric hypersurfaces}},
doi = {10.1017/S1474748014000127},
volume = {14},
year = {2014},
}
@article{7300,
abstract = {Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling.},
author = {Aigner, Daniel and Freunberger, Stefan Alexander and Wilkening, Martin and Saf, Robert and Borisov, Sergey M. and Klimant, Ingo},
issn = {0003-2700},
journal = {Analytical Chemistry},
number = {18},
pages = {9293--9300},
publisher = {ACS},
title = {{Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols}},
doi = {10.1021/ac502513g},
volume = {86},
year = {2014},
}
@article{7301,
abstract = {Several problems arise at the O2 (positive) electrode in the Li-air battery, including solvent/electrode decomposition and electrode passivation by insulating Li2O2. Progress partially depends on exploring the basic electrochemistry of O2 reduction. Here we describe the effect of complexing-cations on the electrochemical reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent with their strong interaction with reduced O2. The complexing-cations also increase the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3 to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+, the complexing-cations also promote the reduction of O2•– to O22–. In the presence of Li+ and complexing-cations, and despite the interaction of the reduced O2 with the latter, SERS confirms that the product is still Li2O2.},
author = {Li, Chunmei and Fontaine, Olivier and Freunberger, Stefan Alexander and Johnson, Lee and Grugeon, Sylvie and Laruelle, Stéphane and Bruce, Peter G. and Armand, Michel},
issn = {1932-7447},
journal = {The Journal of Physical Chemistry C},
number = {7},
pages = {3393--3401},
publisher = {ACS},
title = {{Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent}},
doi = {10.1021/jp4093805},
volume = {118},
year = {2014},
}
@article{7302,
abstract = {Understanding charge carrier transport in Li2O2, the storage material in the non-aqueous Li-O2 battery, is key to the development of this high-energy battery. Here, we studied ionic transport properties and Li self-diffusion in nanocrystalline Li2O2 by conductivity and temperature variable 7Li NMR spectroscopy. Nanostructured Li2O2, characterized by a mean crystallite size of less than 50 nm as estimated from X-ray diffraction peak broadening, was prepared by high-energy ball milling of microcrystalline lithium peroxide with μm sized crystallites. At room temperature the overall conductivity σ of the microcrystalline reference sample turned out to be very low (3.4 × 10−13 S cm−1) which is in agreement with results from temperature-variable 7Li NMR line shape measurements. Ball-milling, however, leads to an increase of σ by approximately two orders of magnitude (1.1 × 10−10 S cm−1); correspondingly, the activation energy decreases from 0.89 eV to 0.82 eV. The electronic contribution σeon, however, is in the order of 9 × 10−12 S cm−1 which makes less than 10% of the total value. Interestingly, 7Li NMR lines of nano-Li2O2 undergo pronounced heterogeneous motional narrowing which manifests in a two-component line shape emerging with increasing temperatures. Most likely, the enhancement in σ can be traced back to the generation of a spin reservoir with highly mobile Li ions; these are expected to reside in the nearest neighbourhood of defects generated or near the structurally disordered and defect-rich interfacial regions formed during mechanical treatment.},
author = {Dunst, A. and Epp, V. and Hanzu, I. and Freunberger, Stefan Alexander and Wilkening, M.},
issn = {1754-5692},
journal = {Energy & Environmental Science},
number = {8},
pages = {2739--2752},
publisher = {RSC},
title = {{Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries}},
doi = {10.1039/c4ee00496e},
volume = {7},
year = {2014},
}
@inbook{7303,
abstract = {The electrolyte in the non-aqueous (aprotic) lithium air battery has a profound influence on the reactions that occur at the anode and cathode, and hence its overall operation on discharge/charge. It must possess a wide range of attributes, exceeding the requirements of electrolytes for Lithium ion batteries by far. The most important additional issues are stability at both anode and cathode in the presence of O2. The known problems with cycling the Li metal/non-aqueous electrolyte interface are further complicated by O2. New and much less understood are the reactions at the O2 cathode/electrolyte interface where the highly reversible formation/decomposition of Li2O2 on discharge/charge is critical for the operation of the non-aqueous lithium air battery. Many aprotic electrolytes exhibit decomposition at the cathode during discharge and charge due to the presence of reactive reduced O2 species affecting potential, capacity and kinetics on discharge and charge, cyclability and calendar life. Identifying suitable electrolytes is one of the key challenges for the non-aqueous lithium air battery at the present time. Following the realisation that cyclability of such cells in the initially used organic carbonate electrolytes is due to back-to-back irreversible reactions the stability of the non-aqueous electrolytes became a major focus of research on rechargeable lithium air batteries. This realisation led to the establishment of a suite of experimental and computational methods capable of screening the stability of electrolytes. These allow for greater mechanistic understanding of the reactivity and guide the way towards designing more stable systems. A range of electrolytes based on ethers, amides, sulfones, ionic liquids and dimethyl sulfoxide have been investigated. All are more stable than the organic carbonates, but not all are equally stable. Even though it was soon realised, by a number of groups, that ethers exhibit side reactions on discharge and charge, they still remain the choice in many studies. To date dimethyl sulfoxide and dimethylacetamide were identified as the most stable electrolytes. In conjunction with the investigation of electrolyte stability the importance of electrode stability became more prominent. The stability of the electrolyte cannot be considered in isolation. Its stability depends on the synergy between electrolyte and electrode. Carbon based electrodes promote electrolyte decomposition and decompose on their own. Although great progress has been made in only a few years, future work on aprotic electrolytes for Li-O2 batteries will need to explore other electrolytes in the quest for yet lower cost, higher safety, stability and low volatility.},
author = {Freunberger, Stefan Alexander and Chen, Yuhui and Bardé, Fanny and Takechi, Kensuke and Mizuno, Fuminori and Bruce, Peter G.},
booktitle = {The Lithium Air Battery: Fundamentals},
editor = {Imanishi, Nobuyuki and Luntz, Alan C. and Bruce, Peter},
isbn = {9781489980618},
pages = {23--58},
publisher = {Springer Nature},
title = {{Nonaqueous Electrolytes}},
doi = {10.1007/978-1-4899-8062-5_2},
year = {2014},
}
@article{7304,
abstract = {Lithium-air batteries have received extraordinary attention recently owing to their theoretical gravimetric energies being considerably higher than those of Li-ion batteries. There are, however, significant challenges to practical implementation, including low energy efficiency, cycle life, and power capability. These are due primarily to the lack of fundamental understanding of oxygen reduction and evolution reaction kinetics and parasitic reactions between oxygen redox intermediate species and nominally inactive battery components such as carbon in the oxygen electrode and electrolytes. In this article, we discuss recent advances in the mechanistic understanding of oxygen redox reactions in nonaqueous electrolytes and the search for electrolytes and electrode materials that are chemically stable in the oxygen electrode. In addition, methods to protect lithium metal against corrosion by water and dendrite formation in aqueous lithium-air batteries are discussed. Further materials innovations lie at the heart of research and development efforts that are needed to enable the development of lithium-oxygen batteries with enhanced round-trip efficiency and cycle life.},
author = {Kwabi, D.G. and Ortiz-Vitoriano, N. and Freunberger, Stefan Alexander and Chen, Y. and Imanishi, N. and Bruce, P.G. and Shao-Horn, Y.},
issn = {0883-7694},
journal = {MRS Bulletin},
number = {5},
pages = {443--452},
publisher = {CUP},
title = {{Materials challenges in rechargeable lithium-air batteries}},
doi = {10.1557/mrs.2014.87},
volume = {39},
year = {2014},
}
@article{7305,
abstract = {When lithium–oxygen batteries discharge, O2 is reduced at the cathode to form solid Li2O2. Understanding the fundamental mechanism of O2 reduction in aprotic solvents is therefore essential to realizing their technological potential. Two different models have been proposed for Li2O2 formation, involving either solution or electrode surface routes. Here, we describe a single unified mechanism, which, unlike previous models, can explain O2 reduction across the whole range of solvents and for which the two previous models are limiting cases. We observe that the solvent influences O2 reduction through its effect on the solubility of LiO2, or, more precisely, the free energy of the reaction LiO2* ⇌ Li(sol)+ + O2−(sol) + ion pairs + higher aggregates (clusters). The unified mechanism shows that low-donor-number solvents are likely to lead to premature cell death, and that the future direction of research for lithium–oxygen batteries should focus on the search for new, stable, high-donor-number electrolytes, because they can support higher capacities and can better sustain discharge.},
author = {Johnson, Lee and Li, Chunmei and Liu, Zheng and Chen, Yuhui and Freunberger, Stefan Alexander and Ashok, Praveen C. and Praveen, Bavishna B. and Dholakia, Kishan and Tarascon, Jean-Marie and Bruce, Peter G.},
issn = {1755-4330},
journal = {Nature Chemistry},
number = {12},
pages = {1091--1099},
publisher = {Springer Nature},
title = {{The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries}},
doi = {10.1038/nchem.2101},
volume = {6},
year = {2014},
}
@article{7361,
abstract = {Bistable switches are fundamental regulatory elements of complex systems, ranging from electronics to living cells. Designed genetic toggle switches have been constructed from pairs of natural transcriptional repressors wired to inhibit one another. The complexity of the engineered regulatory circuits can be increased using orthogonal transcriptional regulators based on designed DNA-binding domains. However, a mutual repressor-based toggle switch comprising DNA-binding domains of transcription-activator-like effectors (TALEs) did not support bistability in mammalian cells. Here, the challenge of engineering a bistable switch based on monomeric DNA-binding domains is solved via the introduction of a positive feedback loop composed of activators based on the same TALE domains as their opposing repressors and competition for the same DNA operator site. This design introduces nonlinearity and results in epigenetic bistability. This principle could be used to employ other monomeric DNA-binding domains such as CRISPR for applications ranging from reprogramming cells to building digital biological memory.},
author = {Lebar, Tina and Bezeljak, Urban and Golob, Anja and Jerala, Miha and Kadunc, Lucija and Pirš, Boštjan and Stražar, Martin and Vučko, Dušan and Zupančič, Uroš and Benčina, Mojca and Forstnerič, Vida and Gaber, Rok and Lonzarić, Jan and Majerle, Andreja and Oblak, Alja and Smole, Anže and Jerala, Roman},
issn = {2041-1723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{A bistable genetic switch based on designable DNA-binding domains}},
doi = {10.1038/ncomms6007},
volume = {5},
year = {2014},
}
@article{7455,
abstract = {The reaction between NiO and (0001)- and ([1\bar102])-oriented Al2O3 single crystals has been investigated on model experimental systems by using the ReflEXAFS technique. Depth-sensitive information is obtained by collecting data above and below the critical angle for total reflection. A systematic protocol for data analysis, based on the recently developed CARD code, was implemented, and a detailed description of the reactive systems was obtained. In particular, for ([1\bar102])-oriented Al2O3, the reaction with NiO is almost complete after heating for 6 h at 1273 K, and an almost uniform layer of spinel is found below a mixed (NiO + spinel) layer at the very upmost part of the sample. In the case of the (0001)-oriented Al2O3, for the same temperature and heating time, the reaction shows a lower advancement degree and a residual fraction of at least 30% NiO is detected in the ReflEXAFS spectra. },
author = {Costanzo, Tommaso and Benzi, Federico and Ghigna, Paolo and Pin, Sonia and Spinolo, Giorgio and d'Acapito, Francesco},
issn = {1600-5775},
journal = {Journal of Synchrotron Radiation},
number = {2},
pages = {395--400},
publisher = {International Union of Crystallography},
title = {{Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS)}},
doi = {10.1107/s1600577513031299},
volume = {21},
year = {2014},
}
@article{7598,
author = {Tan, Shutang and Xue, Hong-Wei},
issn = {2211-1247},
journal = {Cell Reports},
number = {5},
pages = {1692--1702},
publisher = {Elsevier},
title = {{Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5}},
doi = {10.1016/j.celrep.2014.10.047},
volume = {9},
year = {2014},
}
@article{7699,
author = {Sweeney, Lora Beatrice Jaeger and Kelley, Darcy B},
issn = {0959-4388},
journal = {Current Opinion in Neurobiology},
number = {10},
pages = {34--41},
publisher = {Elsevier},
title = {{Harnessing vocal patterns for social communication}},
doi = {10.1016/j.conb.2014.06.006},
volume = {28},
year = {2014},
}
@inbook{7743,
abstract = {Experimental studies have demonstrated that environmental variation can create genotype‐environment interactions (GEIs) in the traits involved in sexual selection. Understanding the genetic architecture of phenotype across environments will require statistical tests that can describe both changes in genetic variance and covariance across environments. This chapter outlines the theoretical framework for the processes of sexual selection in the wild, identifying key parameters in wild systems, and highlighting the potential effects of the environment. It describes the proposed approaches for the estimation of these key parameters in a quantitative genetic framework within naturally occurring pedigreed populations. The chapter provides a worked example for a range of analysis methods. It aims to provide an overview of the analytical methods that can be used to model GEIs for traits involved in sexual selection in naturally occurring pedigreed populations.},
author = {Robinson, Matthew Richard and Qvarnström, Anna},
booktitle = {Genotype-by-Environment Interactions and Sexual Selection},
editor = {Hunt, John and Hosken, David},
isbn = {9780470671795},
pages = {137--168},
publisher = {Wiley},
title = {{Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations}},
doi = {10.1002/9781118912591.ch6},
year = {2014},
}
@article{7744,
author = {Robinson, Matthew Richard and Wray, Naomi R. and Visscher, Peter M.},
issn = {0168-9525},
journal = {Trends in Genetics},
number = {4},
pages = {124--132},
publisher = {Elsevier},
title = {{Explaining additional genetic variation in complex traits}},
doi = {10.1016/j.tig.2014.02.003},
volume = {30},
year = {2014},
}
@article{7768,
abstract = {We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material.},
author = {Lohr, Matthew A. and Still, Tim and Ganti, Raman and Gratale, Matthew D. and Davidson, Zoey S. and Aptowicz, Kevin B. and Goodrich, Carl Peter and Sussman, Daniel M. and Yodh, A. G.},
issn = {1539-3755},
journal = {Physical Review E},
number = {6},
publisher = {American Physical Society},
title = {{Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings}},
doi = {10.1103/physreve.90.062305},
volume = {90},
year = {2014},
}
@article{7769,
abstract = {Athermal packings of soft repulsive spheres exhibit a sharp jamming transition in the thermodynamic limit. Upon further compression, various structural and mechanical properties display clean power-law behavior over many decades in pressure. As with any phase transition, the rounding of such behavior in finite systems close to the transition plays an important role in understanding the nature of the transition itself. The situation for jamming is surprisingly rich: the assumption that jammed packings are isotropic is only strictly true in the large-size limit, and finite-size has a profound effect on the very meaning of jamming. Here, we provide a comprehensive numerical study of finite-size effects in sphere packings above the jamming transition, focusing on stability as well as the scaling of the contact number and the elastic response.},
author = {Goodrich, Carl Peter and Dagois-Bohy, Simon and Tighe, Brian P. and van Hecke, Martin and Liu, Andrea J. and Nagel, Sidney R.},
issn = {1539-3755},
journal = {Physical Review E},
number = {2},
publisher = {American Physical Society},
title = {{Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling}},
doi = {10.1103/physreve.90.022138},
volume = {90},
year = {2014},
}
@article{7770,
abstract = {Packings of frictionless athermal particles that interact only when they overlap experience a jamming transition as a function of packing density. Such packings provide the foundation for the theory of jamming. This theory rests on the observation that, despite the multitude of disordered configurations, the mechanical response to linear order depends only on the distance to the transition. We investigate the validity and utility of such measurements that invoke the harmonic approximation and show that, despite particles coming in and out of contact, there is a well-defined linear regime in the thermodynamic limit.},
author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.},
issn = {1539-3755},
journal = {Physical Review E},
number = {2},
publisher = {American Physical Society},
title = {{Contact nonlinearities and linear response in jammed particulate packings}},
doi = {10.1103/physreve.90.022201},
volume = {90},
year = {2014},
}
@article{7771,
abstract = {In their Letter, Schreck, Bertrand, O'Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is "no harmonic regime in the large system limit for all compressions" and "at jamming onset for any system size." Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. },
author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.},
issn = {0031-9007},
journal = {Physical Review Letters},
number = {4},
publisher = {American Physical Society},
title = {{Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”}},
doi = {10.1103/physrevlett.112.049801},
volume = {112},
year = {2014},
}
@article{7772,
abstract = {Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits in situ variation of particle packing fraction. Bulk, B, and shear, G, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio G/B with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, G and B individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the interparticle interaction from the individual elastic constants and to derive an approximate estimate for the interparticle friction coefficient.},
author = {Still, Tim and Goodrich, Carl Peter and Chen, Ke and Yunker, Peter J. and Schoenholz, Samuel and Liu, Andrea J. and Yodh, A. G.},
issn = {1539-3755},
journal = {Physical Review E},
number = {1},
publisher = {American Physical Society},
title = {{Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions}},
doi = {10.1103/physreve.89.012301},
volume = {89},
year = {2014},
}
@article{7773,
abstract = {For more than a century, physicists have described real solids in terms of perturbations about perfect crystalline order1. Such an approach takes us only so far: a glass, another ubiquitous form of rigid matter, cannot be described in any meaningful sense as a defected crystal2. Is there an opposite extreme to a crystal—a solid with complete disorder—that forms an alternative starting point for understanding real materials? Here, we argue that the solid comprising particles with finite-ranged interactions at the jamming transition3,4,5 constitutes such a limit. It has been shown that the physics associated with this transition can be extended to interactions that are long ranged6. We demonstrate that jamming physics is not restricted to amorphous systems, but dominates the behaviour of solids with surprisingly high order. Just as the free-electron and tight-binding models represent two idealized cases from which to understand electronic structure1, we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming can be set side by side with the physics of crystals to provide an organizing structure for understanding the mechanical properties of solids over the entire spectrum of disorder.},
author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.},
issn = {1745-2473},
journal = {Nature Physics},
number = {8},
pages = {578--581},
publisher = {Springer Nature},
title = {{Solids between the mechanical extremes of order and disorder}},
doi = {10.1038/nphys3006},
volume = {10},
year = {2014},
}
@article{451,
abstract = {We introduce algorithms for the computation of homology, cohomology, and related operations on cubical cell complexes, using the technique based on a chain contraction from the original chain complex to a reduced one that represents its homology. This work is based on previous results for simplicial complexes, and uses Serre’s diagonalization for cubical cells. An implementation in C++ of the introduced algorithms is available at http://www.pawelpilarczyk.com/chaincon/ together with some examples. The paper is self-contained as much as possible, and is written at a very elementary level, so that basic knowledge of algebraic topology should be sufficient to follow it.},
author = {Pawel Pilarczyk and Real, Pedro},
journal = {Advances in Computational Mathematics},
number = {1},
pages = {253 -- 275},
publisher = {Kluwer},
title = {{Computation of cubical homology, cohomology, and (co)homological operations via chain contraction}},
doi = {10.1007/s10444-014-9356-1},
volume = {41},
year = {2014},
}
@article{468,
abstract = {Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance) is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss.},
author = {Cimadom, Arno and Ulloa, Angel and Meidl, Patrick and Zöttl, Markus and Zöttl, Elisabet and Fessl, Birgit and Nemeth, Erwin and Dvorak, Michael and Cunninghame, Francesca and Tebbich, Sabine},
journal = {PLoS One},
number = {9},
publisher = {Public Library of Science},
title = {{Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin's finches}},
doi = {10.1371/journal.pone.0107518},
volume = {9},
year = {2014},
}
@inproceedings{475,
abstract = {First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. },
author = {Aminof, Benjamin and Rubin, Sasha},
booktitle = {Electronic Proceedings in Theoretical Computer Science, EPTCS},
location = {Grenoble, France},
pages = {83 -- 90},
publisher = {Open Publishing Association},
title = {{First cycle games}},
doi = {10.4204/EPTCS.146.11},
volume = {146},
year = {2014},
}
@article{535,
abstract = {Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Krinninger, Sebastian and Nanongkai, Danupon},
journal = {Algorithmica},
number = {3},
pages = {457 -- 492},
publisher = {Springer},
title = {{Polynomial time algorithms for energy games with special weight structures}},
doi = {10.1007/s00453-013-9843-7},
volume = {70},
year = {2014},
}
@article{537,
abstract = {Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.},
author = {Prizak, Roshan and Ezard, Thomas and Hoyle, Rebecca},
journal = {Ecology and Evolution},
number = {15},
pages = {3139 -- 3145},
publisher = {Wiley-Blackwell},
title = {{Fitness consequences of maternal and grandmaternal effects}},
doi = {10.1002/ece3.1150},
volume = {4},
year = {2014},
}
@misc{5411,
abstract = {Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing.
In this paper, we study compositional properties of the IOCO-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the IOCO conformance relation, the resulting methodology can be applied to a broader class of systems.},
author = {Daca, Przemyslaw and Henzinger, Thomas A and Krenn, Willibald and Nickovic, Dejan},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{Compositional specifications for IOCO testing}},
doi = {10.15479/AT:IST-2014-148-v2-1},
year = {2014},
}
@misc{5412,
abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.
We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.
We present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
author = {Chatterjee, Krishnendu and Daca, Przemyslaw and Chmelik, Martin},
issn = {2664-1690},
pages = {31},
publisher = {IST Austria},
title = {{CEGAR for qualitative analysis of probabilistic systems}},
doi = {10.15479/AT:IST-2014-153-v1-1},
year = {2014},
}
@misc{5413,
abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.
We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.
We present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
author = {Chatterjee, Krishnendu and Daca, Przemyslaw and Chmelik, Martin},
issn = {2664-1690},
pages = {33},
publisher = {IST Austria},
title = {{CEGAR for qualitative analysis of probabilistic systems}},
doi = {10.15479/AT:IST-2014-153-v2-2},
year = {2014},
}
@misc{5414,
abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.
We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.
We present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation.
We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
author = {Chatterjee, Krishnendu and Daca, Przemyslaw and Chmelik, Martin},
issn = {2664-1690},
pages = {33},
publisher = {IST Austria},
title = {{CEGAR for qualitative analysis of probabilistic systems}},
doi = {10.15479/AT:IST-2014-153-v3-1},
year = {2014},
}
@misc{5415,
abstract = {Recently there has been a significant effort to add quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, several basic system properties such as average response time cannot be expressed with weighted automata. In this work, we introduce nested weighted automata as a new formalism for expressing important quantitative properties such as average response time. We establish an almost complete decidability picture for the basic decision problems for nested weighted automata, and illustrate its applicability in several domains. },
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
issn = {2664-1690},
pages = {27},
publisher = {IST Austria},
title = {{Nested weighted automata}},
doi = {10.15479/AT:IST-2014-170-v1-1},
year = {2014},
}
@misc{5416,
abstract = {As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.The contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem.},
author = {Henzinger, Thomas A and Otop, Jan},
issn = {2664-1690},
pages = {22},
publisher = {IST Austria},
title = {{Model measuring for hybrid systems}},
doi = {10.15479/AT:IST-2014-171-v1-1},
year = {2014},
}
@misc{5417,
abstract = {We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M'within distance ρ from M satisfy (or violate)φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata.
The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification.
We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved.
We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging.
We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.},
author = {Henzinger, Thomas A and Otop, Jan},
issn = {2664-1690},
pages = {14},
publisher = {IST Austria},
title = {{From model checking to model measuring}},
doi = {10.15479/AT:IST-2014-172-v1-1},
year = {2014},
}
@misc{5418,
abstract = {We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness for parity objectives. The symmetric case of player 1 more informed than player 2 is much more complicated, and we show that already in the case where player 1 has perfect observation, memory of size non-elementary is necessary in general for reachability objectives, and the problem is decidable for safety and reachability objectives. Our results have tight connections with partial-observation stochastic games for which we derive new complexity results.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
issn = {2664-1690},
pages = {18},
publisher = {IST Austria},
title = {{Games with a weak adversary}},
doi = {10.15479/AT:IST-2014-176-v1-1},
year = {2014},
}
@misc{5419,
abstract = {We consider the reachability and shortest path problems on low tree-width graphs, with n nodes, m edges, and tree-width t, on a standard RAM with wordsize W. We use O to hide polynomial factors of the inverse of the Ackermann function. Our main contributions are three fold:
1. For reachability, we present an algorithm that requires O(n·t2·log(n/t)) preprocessing time, O(n·(t·log(n/t))/W) space, and O(t/W) time for pair queries and O((n·t)/W) time for single-source queries. Note that for constant t our algorithm uses O(n·logn) time for preprocessing; and O(n/W) time for single-source queries, which is faster than depth first search/breath first search (after the preprocessing).
2. We present an algorithm for shortest path that requires O(n·t2) preprocessing time, O(n·t) space, and O(t2) time for pair queries and O(n·t) time single-source queries.
3. We give a space versus query time trade-off algorithm for shortest path that, given any constant >0, requires O(n·t2) preprocessing time, O(n·t2) space, and O(n1−·t2) time for pair queries.
Our algorithms improve all existing results, and use very simple data structures.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
issn = {2664-1690},
pages = {34},
publisher = {IST Austria},
title = {{Improved algorithms for reachability and shortest path on low tree-width graphs}},
doi = {10.15479/AT:IST-2014-187-v1-1},
year = {2014},
}
@misc{5420,
abstract = {We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
issn = {2664-1690},
pages = {49},
publisher = {IST Austria},
title = {{The value 1 problem for concurrent mean-payoff games}},
doi = {10.15479/AT:IST-2014-191-v1-1},
year = {2014},
}
@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},
}
@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},
}