@misc{5389,
abstract = {Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.},
author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun},
issn = {2664-1690},
pages = {24},
publisher = {IST Austria},
title = {{Simulation distances}},
doi = {10.15479/AT:IST-2010-0003},
year = {2010},
}
@misc{5390,
abstract = {The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages.},
author = {Chatterjee, Krishnendu and Fijalkow, Nathanaël},
issn = {2664-1690},
pages = {21},
publisher = {IST Austria},
title = {{Topological, automata-theoretic and logical characterization of finitary languages}},
doi = {10.15479/AT:IST-2010-0002},
year = {2010},
}
@misc{5391,
abstract = {Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable.},
author = {Cerny, Pavol and Radhakrishna, Arjun and Zufferey, Damien and Chaudhuri, Swarat and Alur, Rajeev},
issn = {2664-1690},
pages = {27},
publisher = {IST Austria},
title = {{Model checking of linearizability of concurrent list implementations}},
doi = {10.15479/AT:IST-2010-0001},
year = {2010},
}
@article{598,
abstract = {It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes.},
author = {Meyer, Krista and Lin, Shih and Bernecky, Carrie A and Gao, Yuefeng and Taatjes, Dylan},
journal = {Nature Structural and Molecular Biology},
number = {6},
pages = {753 -- 760},
publisher = {Nature Publishing Group},
title = {{P53 activates transcription by directing structural shifts in Mediator}},
doi = {10.1038/nsmb.1816},
volume = {17},
year = {2010},
}
@article{6142,
abstract = {Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.},
author = {Weber, Katherine P. and De, Subhajyoti and Kozarewa, Iwanka and Turner, Daniel J. and Babu, M. Madan and de Bono, Mario},
issn = {1932-6203},
journal = {PLoS ONE},
number = {11},
publisher = {Public Library of Science},
title = {{Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans}},
doi = {10.1371/journal.pone.0013922},
volume = {5},
year = {2010},
}
@article{6320,
abstract = {We study the average order of the divisor function, as it ranges over the values of binary quartic forms that are reducible over ℚ.},
author = {Bretèche, Régis de la and Browning, Timothy D},
journal = {Crelles Journal},
number = {646},
pages = {1--44},
publisher = {Walter de Gruyter GmbH},
title = {{Le problème des diviseurs pour des formes binaires de degré 4}},
doi = {10.1515/crelle.2010.064},
volume = {2010},
year = {2010},
}
@article{7078,
abstract = {We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other.},
author = {Salje, E. K. H. and Safarik, D. J. and Modic, Kimberly A and Gubernatis, J. E. and Cooley, J. C. and Taylor, R. D. and Mihaila, B. and Saxena, A. and Lookman, T. and Smith, J. L. and Fisher, R. A. and Pasternak, M. and Opeil, C. P. and Siegrist, T. and Littlewood, P. B. and Lashley, J. C.},
issn = {1098-0121},
journal = {Physical Review B},
number = {18},
publisher = {APS},
title = {{Tin telluride: A weakly co-elastic metal}},
doi = {10.1103/physrevb.82.184112},
volume = {82},
year = {2010},
}
@article{1465,
abstract = {We prove a generating function formula for the Betti numbers of Nakajima quiver varieties. We prove that it is a q-deformation of the Weyl-Kac character formula. In particular this implies that the constant term of the polynomial counting the number of absolutely indecomposable representations of a quiver equals the multiplicity of a certain weight in the corresponding Kac-Moody algebra, which was conjectured by Kac in 1982.},
author = {Tamas Hausel},
journal = {Inventiones Mathematicae},
number = {1},
pages = {21 -- 37},
publisher = {Springer},
title = {{Kac's conjecture from Nakajima quiver varieties}},
doi = {10.1007/s00222-010-0241-3},
volume = {181},
year = {2010},
}
@article{1466,
abstract = {In Hausel et al. (2008) [10] we presented a conjecture generalizing the Cauchy formula for Macdonald polynomial. This conjecture encodes the mixed Hodge polynomials of the character varieties of representations of the fundamental group of a punctured Riemann surface of genus g. We proved several results which support this conjecture. Here we announce new results which are consequences of those in Hausel et al. (2008) [10].},
author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando},
journal = {Comptes Rendus Mathematique},
number = {3-4},
pages = {131 -- 135},
publisher = {Elsevier},
title = {{Topology of character varieties and representations of quivers}},
doi = {10.1016/j.crma.2010.01.025},
volume = {348},
year = {2010},
}
@inbook{1468,
abstract = {This chapter surveys the motivations, related results, and progress made towards the following problem, raised by Hitchin in 1995: What is the space of L2 harmonic forms on the moduli space of Higgs bundles on a Riemann surface?},
author = {Tamas Hausel},
booktitle = {The Many Facets of Geometry: A Tribute to Nigel Hitchin},
publisher = {Oxford University Press},
title = {{S-Duality in HyperkäHler Hodge Theory}},
doi = {10.1093/acprof:oso/9780199534920.003.0016},
year = {2010},
}