@article{1774,
abstract = {A number of superconducting qubits, such as the transmon or the phase qubit, have an energy level structure with small anharmonicity. This allows for convenient access of higher excited states with similar frequencies. However, special care has to be taken to avoid unwanted higher-level populations when using short control pulses. Here we demonstrate the preparation of arbitrary three level superposition states using optimal control techniques in a transmon. Performing dispersive readout, we extract the populations of all three levels of the qutrit and study the coherence of its excited states. Finally we demonstrate full quantum state tomography of the prepared qutrit states and evaluate the fidelities of a set of states, finding on average 95%.},
author = {Bianchetti, R and Filipp, Stefan and Baur, Matthias P and Johannes Fink and Lang, C and Steffen, L. Kraig and Boissonneault, Maxime and Blais, Alexandre and Wallraff, Andreas},
journal = {Physical Review Letters},
number = {22},
publisher = {American Physical Society},
title = {{Control and tomography of a three level superconducting artificial atom}},
doi = {10.1103/PhysRevLett.105.223601},
volume = {105},
year = {2010},
}
@article{2095,
abstract = {This paper describes a passive stereo system for capturing the 3D geometry of a face in a single-shot under standard light sources. The system is low-cost and easy to deploy. Results are submillimeter accurate and commensurate with those from state-ofthe-art systems based on active lighting, and the models meet the quality requirements of a demanding domain like the movie industry. Recovered models are shown for captures from both high-end cameras in a studio setting and from a consumer binocular-stereo camera, demonstrating scalability across a spectrum of camera deployments, and showing the potential for 3D face modeling to move beyond the professional arena and into the emerging consumer market in stereoscopic photography. Our primary technical contribution is a modification of standard stereo refinement methods to capture pore-scale geometry, using a qualitative approach that produces visually realistic results. The second technical contribution is a calibration method suited to face capture systems. The systemic contribution includes multiple demonstrations of system robustness and quality. These include capture in a studio setup, capture off a consumer binocular-stereo camera, scanning of faces of varying gender and ethnicity and age, capture of highly-transient facial expression, and scanning a physical mask to provide ground-truth validation.},
author = {Beeler, Thabo and Bernd Bickel and Beardsley, Paul A and Sumner, Bob and Groß, Markus S},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{High-quality single-shot capture of facial geometry}},
doi = {10.1145/1778765.1778777},
volume = {29},
year = {2010},
}
@article{2124,
abstract = {We develop a theory of Malliavin calculus for Banach space-valued random variables. Using radonifying operators instead of symmetric tensor products we extend the Wiener-Itô isometry to Banach spaces. In the white noise case we obtain two sided Lp-estimates for multiple stochastic integrals in arbitrary Banach spaces. It is shown that the Malliavin derivative is bounded on vector-valued Wiener-Itô chaoses. Our main tools are decoupling inequalities for vector-valued random variables. In the opposite direction we use Meyer's inequalities to give a new proof of a decoupling result for Gaussian chaoses in UMD Banach spaces.},
author = {Jan Maas},
journal = {Journal of Mathematical Analysis and Applications},
number = {2},
pages = {383 -- 398},
publisher = {Academic Press},
title = {{Malliavin calculus and decoupling inequalities in Banach spaces}},
doi = {10.1016/j.jmaa.2009.08.041},
volume = {363},
year = {2010},
}
@article{2194,
abstract = {We develop an analytic model of vector correlations in rotationally inelastic atom-diatom collisions and test it against the much examined Ar-NO (X2Π) system. Based on the Fraunhofer scattering of matter waves, the model furnishes complex scattering amplitudes needed to evaluate the polarization moments characterizing the quantum stereodynamics. The analytic polarization moments are found to be in an excellent agreement with experimental results and with close-coupling calculations available at thermal energies. The model reveals that the stereodynamics is governed by diffraction from the repulsive core of the Ar-NO potential, which can be characterized by a single Legendre moment.},
author = {Mikhail Lemeshko and Friedrich, Břetislav},
journal = {Physical Chemistry Chemical Physics},
number = {5},
pages = {1038 -- 1041},
publisher = {Royal Society of Chemistry},
title = {{An analytic model of the stereodynamics of rotationally inelastic molecular collisions}},
doi = {10.1039/B920899B },
volume = {12},
year = {2010},
}
@article{2195,
abstract = {Following upon our recent work on vector correlations in the Ar-NO collisions [Lemeshko and Friedrich, Phys. Chem. Chem. Phys. 12, 1038 (2010)], we compare model results with close-coupling calculations for a range of channels and collision energies for the He-NO system. The striking agreement between the model and exact polarization moments indicates that the stereodynamics of rotationally inelastic atom-molecule collisions at thermal energies is governed by diffraction of matter waves from a two-dimensional repulsive core of the atom-molecule potential. Furthermore, the model polarization moments characterizing the He-NO, He- O2, He-OH, and He-CaH stereodynamics are found to coalesce into a single, distinctive pattern, which can serve as a "fingerprint" to identify diffraction-driven stereodynamics in future work. },
author = {Mikhail Lemeshko and Jambrina, Pablo G and De Miranda, Marcelo P and Friedrich, Břetislav},
journal = {Journal of Chemical Physics},
number = {16},
publisher = {American Institute of Physics},
title = {{Communications: When diffraction rules the stereodynamics of rotationally inelastic collisions}},
doi = {10.1063/1.3386530},
volume = {132},
year = {2010},
}
@article{2196,
abstract = {We evaluate the shifts imparted to vibrational and rotational levels of a linear molecule by a nonresonant laser field at intensities of up to 10 12 W/cm2. Both types of shift are found to be either positive or negative, depending on the initial rotational state acted upon by the field. An adiabatic field-molecule interaction imparts a rotational energy shift which is negative and exceeds the concomitant positive vibrational shift by a few orders of magnitude. The rovibrational states are thus pushed downward in such a field. A nonresonant pulsed laser field that interacts nonadiabatically with the molecule is found to impart rotational and vibrational shifts of the same order of magnitude. The nonadiabatic energy transfer occurs most readily at a pulse duration which amounts to about a tenth of the molecule's rotational period and vanishes when the sudden regime is attained for shorter pulses. We applied our treatment to the much-studied 87Rb2 molecule in the last bound vibrational levels of its lowest singlet and triplet electronic states. Our calculations indicate that 15 and 1.5 ns laser pulses of an intensity in excess of 5 × 109 W/cm2 are capable of dissociating the molecule due to the vibrational shift. Lesser shifts can be used to fine-tune the rovibrational levels and thereby affect collisional resonances by the nonresonant light. The energy shifts due to laser intensities of 109 W/cm2 may be discernible spectroscopically, with a 10 MHz resolution.},
author = {Mikhail Lemeshko and Friedrich, Břetislav},
journal = {Journal of Physical Chemistry A},
number = {36},
pages = {9848 -- 9854},
publisher = {American Chemical Society},
title = {{Fine-tuning molecular energy levels by nonresonant laser pulses}},
doi = {10.1021/jp1032299},
volume = {114},
year = {2010},
}
@article{2197,
abstract = {We present an analytic model of the refractive index for matter waves propagating through atomic or molecular gases. The model, which combines the Wentzel-Kramers-Brillouin (WKB) treatment of the long-range attraction with the Fraunhofer model treatment of the short-range repulsion, furnishes a refractive index in compelling agreement with recent experiments of Jacquey [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.98.240405 98, 240405 (2007)] on Li atom matter waves passing through dilute noble gases. We show that the diffractive contribution, which arises from scattering by a two-dimensional "hard core" of the potential, is essential for obtaining a correct imaginary part of the refractive index.},
author = {Mikhail Lemeshko and Friedrich, Břetislav},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {2},
publisher = {American Physical Society},
title = {{Multiple scattering of matter waves: An analytic model of the refractive index for atomic and molecular gases}},
doi = {10.1103/PhysRevA.82.022711},
volume = {82},
year = {2010},
}
@inproceedings{488,
abstract = {Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of "regular" transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. },
author = {Alur, Rajeev and Cerny, Pavol},
location = {Chennai, India},
pages = {1 -- 12},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Expressiveness of streaming string transducers}},
doi = {10.4230/LIPIcs.FSTTCS.2010.1},
volume = {8},
year = {2010},
}
@inproceedings{489,
abstract = {Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies.},
author = {Cristau, Julien and David, Claire and Horn, Florian},
booktitle = {Proceedings of GandALF 2010},
location = {Minori, Amalfi Coast, Italy},
pages = {30 -- 39},
publisher = {Open Publishing Association},
title = {{How do we remember the past in randomised strategies? }},
doi = {10.4204/EPTCS.25.7},
volume = {25},
year = {2010},
}
@misc{5388,
abstract = {We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.
We show that for worst-case performance, the problem can be modeled
as a 2-player graph game with quantitative (limit-average) objectives, and
for average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.
We have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements.},
author = {Chatterjee, Krishnendu and Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun and Singh, Rohit},
issn = {2664-1690},
pages = {17},
publisher = {IST Austria},
title = {{Quantitative synthesis for concurrent programs}},
doi = {10.15479/AT:IST-2010-0004},
year = {2010},
}
@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},
}
@article{1044,
abstract = {Control over all internal and external degrees of freedom of molecules at the level of single quantum states will enable a series of fundamental studies in physics and chemistry1,2. In particular, samples of ground-state molecules at ultralow temperatures and high number densities will facilitate new quantum-gas studies3 and future applications in quantum information science4. However, high phase-space densities for molecular samples are not readily attainable because efficient cooling techniques such as laser cooling are lacking. Here we produce an ultracold and dense sample of molecules in a single hyperfine level of the rovibronic ground state with each molecule individually trapped in the motional ground state of an optical lattice well. Starting from a zero-temperature atomic Mott-insulator state with optimized double-site occupancy6, weakly bound dimer molecules are efficiently associated on a Feshbach resonance7 and subsequently transferred to the rovibronic ground state by a stimulated four-photon process with >50% efficiency. The molecules are trapped in the lattice and have a lifetime of 8 s. Our results present a crucial step towards Bose-Einstein condensation of ground-state molecules and, when suitably generalized to polar heteronuclear molecules, the realization of dipolar quantum-gas phases in optical lattices8-10.},
author = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Hart, Russell and Aldegunde, Jesus and Hutson, Jeremy and Nägerl, Hanns},
journal = {Nature Physics},
number = {4},
pages = {265 -- 270},
publisher = {Nature Publishing Group},
title = {{An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice}},
doi = {10.1038/nphys1533},
volume = {6},
year = {2010},
}
@article{1045,
abstract = {We report on the observation of confinement-induced resonances in strongly interacting quantum-gas systems with tunable interactions for one- and two-dimensional geometry. Atom-atom scattering is substantially modified when the s-wave scattering length approaches the length scale associated with the tight transversal confinement, leading to characteristic loss and heating signatures. Upon introducing an anisotropy for the transversal confinement we observe a splitting of the confinement-induced resonance. With increasing anisotropy additional resonances appear. In the limit of a two-dimensional system we find that one resonance persists.},
author = {Haller, Elmar and Mark, Manfred and Hart, Russell and Danzl, Johann G and Reichsöllner, Lukas and Melezhik, Vladimir and Schmelcher, Peter and Nägerl, Hanns},
journal = {Physical Review Letters},
number = {15},
publisher = {American Physical Society},
title = {{Confinement-induced resonances in low-dimensional quantum systems}},
doi = {10.1103/PhysRevLett.104.153203},
volume = {104},
year = {2010},
}
@article{1047,
abstract = {Particles in a perfect lattice potential perform Bloch oscillations when subject to a constant force, leading to localization and preventing conductivity. For a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass oscillations in position space with a displacement across hundreds of lattice sites when we add a periodic modulation to the force near the Bloch frequency. We study the dependence of these "super" Bloch oscillations on lattice depth, modulation amplitude, and modulation frequency and show that they provide a means to induce linear transport in a dissipation-free lattice.},
author = {Haller, Elmar and Hart, Russell and Mark, Manfred and Danzl, Johann G and Reichsöllner, Lukas and Nägerl, Hanns},
journal = {Physical Review Letters},
number = {20},
publisher = {American Physical Society},
title = {{Inducing transport in a dissipation-free lattice with super bloch oscillations}},
doi = {10.1103/PhysRevLett.104.200403},
volume = {104},
year = {2010},
}
@article{1049,
abstract = {Quantum many-body systems can have phase transitions even at zero temperature; fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to thermal effects, drive the system from one phase to another. Typically, during the transition the relative strength of two competing terms in the systemĝ€™s Hamiltonian changes across a finite critical value. A well-known example is the Mottĝ€" Hubbard quantum phase transition from a superfluid to an insulating phase, which has been observed for weakly interacting bosonic atomic gases. However, for strongly interacting quantum systems confined to lower-dimensional geometry, a novel type of quantum phase transition may be induced and driven by an arbitrarily weak perturbation to the Hamiltonian. Here we observe such an effectĝ€"the sineĝ€"Gordon quantum phase transition from a superfluid Luttinger liquid to a Mott insulatorĝ€ "in a one-dimensional quantum gas of bosonic caesium atoms with tunable interactions. For sufficiently strong interactions, the transition is induced by adding an arbitrarily weak optical lattice commensurate with the atomic granularity, which leads to immediate pinning of the atoms. We map out the phase diagram and find that our measurements in the strongly interacting regime agree well with a quantum field description based on the exactly solvable sineĝ€"Gordon model. We trace the phase boundary all the way to the weakly interacting regime, where we find good agreement with the predictions of the one-dimensional Boseĝ€"Hubbard model. Our results open up the experimental study of quantum phase transitions, criticality and transport phenomena beyond Hubbard-type models in the context of ultracold gases.},
author = {Haller, Elmar and Hart, Russell and Mark, Manfred and Danzl, Johann G and Reichsöllner, Lukas and Gustavsson, Mattias and Dalmonte, Marcello and Pupillo, Guido and Nägerl, Hanns},
journal = {Nature},
number = {7306},
pages = {597 -- 600},
publisher = {Nature Publishing Group},
title = {{Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons}},
doi = {10.1038/nature09259},
volume = {466},
year = {2010},
}
@article{9012,
abstract = {In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.},
author = {Palacci, Jérémie A and Abécassis, Benjamin and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric},
issn = {10797114},
journal = {Physical Review Letters},
number = {13},
publisher = {American Physical Society},
title = {{Colloidal motility and pattern formation under rectified diffusiophoresis}},
doi = {10.1103/physrevlett.104.138302},
volume = {104},
year = {2010},
}
@article{9013,
abstract = {In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.},
author = {Palacci, Jérémie A and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric},
issn = {10797114},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society },
title = {{Sedimentation and effective temperature of active colloidal suspensions}},
doi = {10.1103/physrevlett.105.088304},
volume = {105},
year = {2010},
}
@article{9146,
abstract = {The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude.
Clausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1.
Surface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.},
author = {O’Gorman, P A and MULLER, Caroline J},
issn = {1748-9326},
journal = {Environmental Research Letters},
keywords = {Renewable Energy, Sustainability and the Environment, Public Health, Environmental and Occupational Health, General Environmental Science},
number = {2},
publisher = {IOP Publishing},
title = {{How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?}},
doi = {10.1088/1748-9326/5/2/025207},
volume = {5},
year = {2010},
}
@inproceedings{3719,
abstract = {The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.},
author = {Feret, Jérôme and Henzinger, Thomas A and Koeppl, Heinz and Petrov, Tatjana},
location = {Jena, Germany},
pages = {142--161},
publisher = {Open Publishing Association},
title = {{Lumpability abstractions of rule-based systems}},
volume = {40},
year = {2010},
}
@unpublished{3743,
abstract = {These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.},
author = {Gasper Tkacik},
booktitle = {ArXiv},
pages = {1 -- 52},
publisher = {ArXiv},
title = {{From statistical mechanics to information theory: understanding biophysical information-processing systems}},
volume = {q-bio.MN},
year = {2010},
}
@article{3748,
abstract = {The chemotaxis signalling network in Escherichia coli that controls the locomotion of bacteria is a classic model system for signal transduction1, 2. This pathway modulates the behaviour of flagellar motors to propel bacteria towards sources of chemical attractants. Although this system relaxes to a steady state in response to environmental changes, the signalling events within the chemotaxis network are noisy and cause large temporal variations of the motor behaviour even in the absence of stimulus3. That the same signalling network governs both behavioural variability and cellular response raises the question of whether these two traits are independent. Here, we experimentally establish a fluctuation–response relationship in the chemotaxis system of living bacteria. Using this relationship, we demonstrate the possibility of inferring the cellular response from the behavioural variability measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour of individual bacterial motors, we found that variability scales linearly with the response time for different functioning states of the cell. This study highlights that the fundamental relationship between fluctuation and response is not constrained to physical systems at thermodynamic equilibrium4 but is extensible to living cells5. Such a relationship not only implies that behavioural variability and cellular response can be coupled traits, but it also provides a general framework within which we can examine how the selection of a network design shapes this interdependence},
author = {Park, Heungwon and Pontius, William and Calin Guet and Marko, John F and Emonet,Thierry and Cluzel,Philippe},
journal = {Nature},
pages = {819 -- 823},
publisher = {Nature Publishing Group},
title = {{Interdependence of behavioural variability and response to small stimuli in bacteria}},
doi = {10.1038/nature09551},
volume = {468},
year = {2010},
}
@article{3749,
abstract = {In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to L: -aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio.},
author = {Park, Heungwon and Calin Guet and Emonet,Thierry and Cluzel,Philippe},
journal = {Current Microbiology},
number = {3},
pages = {764 -- 769},
publisher = {Springer},
title = {{Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay}},
doi = {10.1007/s00284-010-9778-z},
volume = {62},
year = {2010},
}
@article{3772,
author = {Barton, Nicholas H},
journal = {PLoS Genetics},
number = {6},
publisher = {Public Library of Science},
title = {{Understanding adaptation in large populations}},
doi = {10.1371/journal.pgen.1000987},
volume = {6},
year = {2010},
}
@article{3773,
abstract = {If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.},
author = {Barton, Nicholas H},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1547},
pages = {1825 -- 1840},
publisher = {Royal Society},
title = {{What role does natural selection play in speciation?}},
doi = {10.1098/rstb.2010.0001},
volume = {365},
year = {2010},
}
@article{3776,
abstract = {The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps.},
author = {Barton, Nicholas H},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1552},
pages = {2559 -- 2569},
publisher = {Royal Society},
title = {{Genetic linkage and natural selection}},
doi = {10.1098/rstb.2010.0106},
volume = {365},
year = {2010},
}
@article{3777,
abstract = {Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.},
author = {Barton, Nicholas H},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1544},
pages = {1281 -- 1294},
publisher = {Royal Society},
title = {{Mutation and the evolution of recombination}},
doi = {10.1098/rstb.2009.0320},
volume = {365},
year = {2010},
}
@article{3779,
abstract = {Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity.},
author = {Rosas, Ulises and Barton, Nicholas H and Copsey, Lucy and Barbier De Reuille, Pierre and Coen, Enrico},
journal = {PLoS Biology},
number = {7},
publisher = {Public Library of Science},
title = {{Cryptic variation between species and the basis of hybrid performance}},
doi = {10.1371/journal.pbio.1000429},
volume = {8},
year = {2010},
}
@article{3787,
abstract = {DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided.},
author = {Palero, Ferran and Hall, Sally and Clark, Paul and Johnston, David and Mackenzie Dodds, Jackie and Thatje, Sven},
journal = {Scientia Marina},
number = {3},
pages = {465 -- 470},
publisher = {Consejo Superior de Investigaciones Científicas},
title = {{DNA extraction from formalin-fixed tissue: new light from the deep sea}},
doi = {10.3989/scimar.2010.74n3465},
volume = {74},
year = {2010},
}
@article{3790,
abstract = {Cell shape and motility are primarily controlled by cellular mechanics. The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation. However, little is known about the actual function of membrane-to-cortex attachment (MCA) in cell protrusion formation and migration, in particular in the context of the developing embryo. Here, we use a multidisciplinary approach to study MCA in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells, which migrate using a combination of different protrusion types, namely, lamellipodia, filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity of molecules linking the cortex to the membrane and measuring resulting changes in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors increases the proportion of cellular blebs and reduces the directionality of cell migration. We propose that MCA is a key parameter controlling the relative proportions of different cell protrusion types in mesendoderm progenitors, and thus is key in controlling directed migration during gastrulation.},
author = {Diz Muñoz, Alba and Krieg, Michael and Bergert, Martin and Ibarlucea Benitez, Itziar and Müller, Daniel and Paluch, Ewa and Heisenberg, Carl-Philipp J},
journal = {PLoS Biology},
number = {11},
publisher = {Public Library of Science},
title = {{Control of directed cell migration in vivo by membrane-to-cortex attachment}},
doi = {10.1371/journal.pbio.1000544},
volume = {8},
year = {2010},
}
@inproceedings{3793,
abstract = {Recent progress in per-pixel object class labeling of natural images can be attributed to the use of multiple types of image features and sound statistical learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently used for their ability to represent interactions between random variables. Despite their popularity in computer vision, parameter learning for CRFs has remained difficult, popular approaches being cross-validation and piecewise training.
In this work, we propose a simple yet expressive tree-structured CRF based on a recent hierarchical image segmentation method. Our model combines and weights multiple image features within a hierarchical representation and allows simple and efficient globally-optimal learning of ≈ 105 parameters. The tractability of our model allows us to pose and answer some of the open questions regarding parameter learning applying to CRF-based approaches. The key findings for learning CRF models are, from the obvious to the surprising, i) multiple image features always help, ii) the limiting dimension with respect to current models is the amount of training data, iii) piecewise training is competitive, iv) current methods for max-margin training fail for models with many parameters.
},
author = {Nowozin, Sebastian and Gehler, Peter and Lampert, Christoph},
location = {Heraklion, Crete, Greece},
pages = {98 -- 111},
publisher = {Springer},
title = {{On parameter learning in CRF-based approaches to object class image segmentation}},
doi = {10.1007/978-3-642-15567-3_8},
volume = {6316},
year = {2010},
}
@inbook{3795,
abstract = {The (apparent) contour of a smooth mapping from a 2-manifold to the plane, f: M → R2 , is the set of critical values, that is, the image of the points at which the gradients of the two component functions are linearly dependent. Assuming M is compact and orientable and measuring difference with the erosion distance, we prove that the contour is stable.},
author = {Edelsbrunner, Herbert and Morozov, Dmitriy and Patel, Amit},
booktitle = {Topological Data Analysis and Visualization: Theory, Algorithms and Applications},
pages = {27 -- 42},
publisher = {Springer},
title = {{The stability of the apparent contour of an orientable 2-manifold}},
doi = {10.1007/978-3-642-15014-2_3},
year = {2010},
}
@article{3831,
abstract = {Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in feedforward and feedback inhibition in the hippocampus. However, the dendritic mechanisms underlying rapid interneuron recruitment have remained unclear. To quantitatively address this question, we developed detailed passive cable models of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings and complete morphologic reconstructions. Both specific membrane capacitance and axial resistivity were comparable to those of pyramidal neurons, but the average somatodendritic specific membrane resistance (R(m)) was substantially lower in BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons. Further computational analysis revealed that these unique cable properties accelerate the time course of synaptic potentials at the soma in response to fast inputs, while boosting the efficacy of slow distal inputs. These properties will facilitate both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits.},
author = {Norenberg, Anja and Hua Hu and Vida, Imre and Bartos, Marlene and Peter Jonas},
journal = {PNAS},
number = {2},
pages = {894 -- 9},
publisher = {National Academy of Sciences},
title = {{Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons}},
doi = {10.1073/pnas.0910716107},
volume = {107},
year = {2010},
}
@article{3832,
abstract = {A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates desensitization and prolongs recovery from desensitization. CKAMP44 is highly expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR subunits control the time course of signaling at glutamatergic synapses.},
author = {Guzmán, José and Jonas, Peter M},
journal = {Neuron},
number = {1},
pages = {8 -- 10},
publisher = {Elsevier},
title = {{Beyond TARPs: The growing list of auxiliary AMPAR subunits}},
doi = {10.1016/j.neuron.2010.04.003},
volume = {66},
year = {2010},
}
@article{3834,
abstract = {Background
The chemical master equation (CME) is a system of ordinary differential equations that describes the evolution of a network of chemical reactions as a stochastic process. Its solution yields the probability density vector of the system at each point in time. Solving the CME numerically is in many cases computationally expensive or even infeasible as the number of reachable states can be very large or infinite. We introduce the sliding window method, which computes an approximate solution of the CME by performing a sequence of local analysis steps. In each step, only a manageable subset of states is considered, representing a "window" into the state space. In subsequent steps, the window follows the direction in which the probability mass moves, until the time period of interest has elapsed. We construct the window based on a deterministic approximation of the future behavior of the system by estimating upper and lower bounds on the populations of the chemical species.
Results
In order to show the effectiveness of our approach, we apply it to several examples previously described in the literature. The experimental results show that the proposed method speeds up the analysis considerably, compared to a global analysis, while still providing high accuracy.
Conclusions
The sliding window method is a novel approach to address the performance problems of numerical algorithms for the solution of the chemical master equation. The method efficiently approximates the probability distributions at the time points of interest for a variety of chemically reacting systems, including systems for which no upper bound on the population sizes of the chemical species is known a priori.},
author = {Wolf, Verena and Goel, Rushil and Mateescu, Maria and Henzinger, Thomas A},
journal = {BMC Systems Biology},
number = {42},
pages = {1 -- 19},
publisher = {BioMed Central},
title = {{Solving the chemical master equation using sliding windows}},
doi = {10.1186/1752-0509-4-42},
volume = {4},
year = {2010},
}
@inproceedings{3838,
abstract = {We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe net- works of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is based on the construction of a stochastic hybrid model in which certain discrete random variables of the original Markov chain are approximated by continuous deterministic variables. We compute the solution of the stochastic hybrid model using a numerical algorithm that discretizes time and in each step performs a mutual update of the transient prob- ability distribution of the discrete stochastic variables and the values of the continuous deterministic variables. We im- plemented the algorithm and we demonstrate its usefulness and efficiency on several case studies from systems biology.},
author = {Henzinger, Thomas A and Mateescu, Maria and Mikeev, Linar and Wolf, Verena},
location = {Trento, Italy},
pages = {55 -- 65},
publisher = {Springer},
title = {{Hybrid numerical solution of the chemical master equation}},
doi = {10.1145/1839764.1839772},
year = {2010},
}
@inproceedings{3839,
abstract = {We present a loop property generation method for loops iterating over multi-dimensional arrays. When used on matrices, our method is able to infer their shapes (also called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties, we first transform a nested loop iterating over a multi- dimensional array into an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants for each unnested loop using a generalization of a recurrence-based invariant generation technique. These loop invariants give us conditions on matrices from which we can derive matrix types automatically us- ing theorem provers. Invariant generation is implemented in the software package Aligator and types are derived by theorem provers and SMT solvers, including Vampire and Z3. When run on the Java matrix package JAMA, our tool was able to infer automatically all matrix types describing the matrix shapes guaranteed by JAMA’s API.},
author = {Henzinger, Thomas A and Hottelier, Thibaud and Kovács, Laura and Voronkov, Andrei},
location = {Madrid, Spain},
pages = {163 -- 179},
publisher = {Springer},
title = {{Invariant and type inference for matrices}},
doi = {10.1007/978-3-642-11319-2_14},
volume = {5944},
year = {2010},
}
@article{3842,
abstract = {Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformization technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this paper we present an on-the-fly variant of uniformization, where we improve the original algorithm at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.},
author = {Didier, Frédéric and Henzinger, Thomas A and Mateescu, Maria and Wolf, Verena},
journal = {IET Systems Biology},
number = {6},
pages = {441 -- 452},
publisher = {Institution of Engineering and Technology},
title = {{Fast adaptive uniformization of the chemical master equation}},
doi = {10.1049/iet-syb.2010.0005},
volume = {4},
year = {2010},
}
@inproceedings{3845,
abstract = {This paper presents Aligators, a tool for the generation of universally quantified array invariants. Aligators leverages recurrence solving and algebraic techniques to carry out inductive reasoning over array content. The Aligators’ loop extraction module allows treatment of multi-path loops by exploiting their commutativity and serializability properties. Our experience in applying Aligators on a collection of loops from open source software projects indicates the applicability of recurrence and algebraic solving techniques for reasoning about arrays.},
author = {Henzinger, Thomas A and Hottelier, Thibaud and Kovács, Laura and Rybalchenko, Andrey},
location = {Yogyakarta, Indonesia},
pages = {348 -- 356},
publisher = {Springer},
title = {{Aligators for arrays}},
doi = {10.1007/978-3-642-16242-8_25},
volume = {6397},
year = {2010},
}
@inproceedings{3847,
abstract = {The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these reactions can be modeled as transitions of a Markov chain. SABRE accepts as input the formalism of guarded commands, which it interprets either as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic analysis by directly computing a mean-field approximation of the system under study. We illustrate the different functionalities of SABRE by means of biological case studies.},
author = {Didier, Frédéric and Henzinger, Thomas A and Mateescu, Maria and Wolf, Verena},
location = {Williamsburg, USA},
pages = {193 -- 194},
publisher = {IEEE},
title = {{SABRE: A tool for the stochastic analysis of biochemical reaction networks}},
doi = {10.1109/QEST.2010.33},
year = {2010},
}
@inproceedings{3849,
abstract = {Using ideas from persistent homology, the robustness of a level set of a real-valued function is defined in terms of the magnitude of the perturbation necessary to kill the classes. Prior work has shown that the homology and robustness information can be read off the extended persistence diagram of the function. This paper extends these results to a non-uniform error model in which perturbations vary in their magnitude across the domain.},
author = {Bendich, Paul and Edelsbrunner, Herbert and Kerber, Michael and Patel, Amit},
location = {Brno, Czech Republic},
pages = {12 -- 23},
publisher = {Springer},
title = {{Persistent homology under non-uniform error}},
doi = {10.1007/978-3-642-15155-2_2},
volume = {6281},
year = {2010},
}
@article{385,
abstract = {Scanning tunneling spectroscopy studies on high-quality Bi2Te3 crystals exhibit perfect correspondence to angle-resolved photoemission spectroscopy data, hence enabling identification of different regimes measured in the local density of states (LDOS). Oscillations of LDOS near a step are analyzed. Within the main part of the surface band oscillations are strongly damped, supporting the hypothesis of topological protection. At higher energies, as the surface band becomes concave, oscillations appear, dispersing with a wave vector that may result from a hexagonal warping term. },
author = {Alpichshev, Zhanybek and Analytis, James and Chu, Jiunhaw and Fisher, Ian and Chen, Yulin and Shen, Zhixun and Fang, Aiping and Kapitulnik, Aharon},
journal = {Physical Review Letters},
number = {1},
publisher = {American Physical Society},
title = {{STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects}},
doi = {10.1103/PhysRevLett.104.016401},
volume = {104},
year = {2010},
}
@inproceedings{3851,
abstract = {Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objective. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is polynomially equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
location = {Bordeaux, France},
pages = {599 -- 610},
publisher = {Springer},
title = {{Energy parity games}},
doi = {10.1007/978-3-642-14162-1_50},
volume = {6199},
year = {2010},
}
@inproceedings{3852,
abstract = {We introduce two-level discounted games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted game and the lower level game is an undiscounted reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. We show the existence of pure memoryless optimal strategies for both players and an ordered field property for such games. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted games can be decided in NP intersected coNP. We also give an alternate strategy improvement algorithm to compute the value. },
author = {Chatterjee, Krishnendu and Majumdar, Ritankar},
location = {Minori, Italy},
pages = {22 -- 29},
publisher = {EPTCS},
title = {{Discounting in games across time scales}},
doi = {10.4204/EPTCS.25.6},
volume = {25},
year = {2010},
}
@inproceedings{3853,
abstract = {Quantitative languages are an extension of boolean languages that assign to each word a real number. Mean-payoff automata are finite automata with numerical weights on transitions that assign to each infinite path the long-run average of the transition weights. When the mode of branching of the automaton is deterministic, nondeterministic, or alternating, the corresponding class of quantitative languages is not robust as it is not closed under the pointwise operations of max, min, sum, and numerical complement. Nondeterministic and alternating mean-payoff automata are not decidable either, as the quantitative generalization of the problems of universality and language inclusion is undecidable. We introduce a new class of quantitative languages, defined by mean-payoff automaton expressions, which is robust and decidable: it is closed under the four pointwise operations, and we show that all decision problems are decidable for this class. Mean-payoff automaton expressions subsume deterministic meanpayoff automata, and we show that they have expressive power incomparable to nondeterministic and alternating mean-payoff automata. We also present for the first time an algorithm to compute distance between two quantitative languages, and in our case the quantitative languages are given as mean-payoff automaton expressions.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Edelsbrunner, Herbert and Henzinger, Thomas A and Rannou, Philippe},
location = {Paris, France},
pages = {269 -- 283},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Mean-payoff automaton expressions}},
doi = {10.1007/978-3-642-15375-4_19},
volume = {6269},
year = {2010},
}
@inproceedings{3855,
abstract = {We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with parity objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observations. We consider qualitative analysis problems: given a POMDP with a parity objective, decide whether there exists an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis problem for POMDPs with parity objectives and its subclasses: safety, reachability, Büchi, and coBüchi objectives. We establish several upper and lower bounds that were not known in the literature. Second, we give optimal bounds (matching upper and lower bounds) for the memory required by pure and randomized observation-based strategies for each class of objectives.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
location = {Brno, Czech Republic},
pages = {258 -- 269},
publisher = {Springer},
title = {{Qualitative analysis of partially-observable Markov Decision Processes}},
doi = {10.1007/978-3-642-15155-2_24},
volume = {6281},
year = {2010},
}
@inproceedings{3856,
abstract = {We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (players interact simultaneously); and (b) turn-based (players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. We present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function (probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. },
author = {Chatterjee, Krishnendu and Doyen, Laurent and Gimbert, Hugo and Henzinger, Thomas A},
location = {Brno, Czech Republic},
pages = {246 -- 257},
publisher = {Springer},
title = {{Randomness for free}},
doi = {10.1007/978-3-642-15155-2_23},
volume = {6281},
year = {2010},
}
@inproceedings{3858,
abstract = {We consider two-player zero-sum games on graphs. On the basis of the information available to the players these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have com- plete view of the game). We survey the complexity results for the problem of de- ciding the winner in various classes of partial-observation games with ω-regular winning conditions specified as parity objectives. We present a reduction from the class of parity objectives that depend on sequence of states of the game to the sub-class of parity objectives that only depend on the sequence of observations. We also establish that partial-observation acyclic games are PSPACE-complete.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
location = {Yogyakarta, Indonesia},
pages = {1 -- 14},
publisher = {Springer},
title = {{The complexity of partial-observation parity games}},
doi = {10.1007/978-3-642-16242-8_1},
volume = {6397},
year = {2010},
}
@inproceedings{3860,
abstract = {In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Generalized mean-payoff and energy games replace individual weights by tuples, and the limit average (resp. running sum) of each coordinate must be (resp. remain) nonnegative. These games have applications in the synthesis of resource-bounded processes with multiple resources. We prove the finite-memory determinacy of generalized energy games and show the inter- reducibility of generalized mean-payoff and energy games for finite-memory strategies. We also improve the computational complexity for solving both classes of games with finite-memory strategies: while the previously best known upper bound was EXPSPACE, and no lower bound was known, we give an optimal coNP-complete bound. For memoryless strategies, we show that the problem of deciding the existence of a winning strategy for the protagonist is NP-complete.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A and Raskin, Jean},
location = {Chennai, India},
pages = {505 -- 516},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Generalized mean-payoff and energy games}},
doi = {10.4230/LIPIcs.FSTTCS.2010.505},
volume = {8},
year = {2010},
}
@article{3861,
abstract = {We introduce strategy logic, a logic that treats strategies in two-player games as explicit first-order objects. The explicit treatment of strategies allows us to specify properties of nonzero-sum games in a simple and natural way. We show that the one-alternation fragment of strategy logic is strong enough to express the existence of Nash equilibria and secure equilibria, and subsumes other logics that were introduced to reason about games, such as ATL, ATL*, and game logic. We show that strategy logic is decidable, by constructing tree automata that recognize sets of strategies. While for the general logic, our decision procedure is nonelementary, for the simple fragment that is used above we show that the complexity is polynomial in the size of the game graph and optimal in the size of the formula (ranging from polynomial to 2EXPTIME depending on the form of the formula).},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Piterman, Nir},
journal = {Information and Computation},
number = {6},
pages = {677 -- 693},
publisher = {Elsevier},
title = {{Strategy logic}},
doi = {10.1016/j.ic.2009.07.004},
volume = {208},
year = {2010},
}
@article{3862,
abstract = {Quantitative generalizations of classical languages, which assign to each word a real number instead of a Boolean value, have applications in modeling resource-constrained computation. We use weighted automata (finite automata with transition weights) to define several natural classes of quantitative languages over finite and infinite words; in particular, the real value of an infinite run is computed as the maximum, limsup, liminf, limit average, or discounted sum of the transition weights. We define the classical decision problems of automata theory (emptiness, universality, language inclusion, and language equivalence) in the quantitative setting and study their computational complexity. As the decidability of the language-inclusion problem remains open for some classes of weighted automata, we introduce a notion of quantitative simulation that is decidable and implies language inclusion. We also give a complete characterization of the expressive power of the various classes of weighted automata. In particular, we show that most classes of weighted automata cannot be determinized.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
journal = {ACM Transactions on Computational Logic (TOCL)},
number = {4},
publisher = {ACM},
title = {{Quantitative languages}},
doi = {10.1145/1805950.1805953},
volume = {11},
year = {2010},
}
@article{3863,
abstract = {We consider two-player parity games with imperfect information in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. One major obstacle in adapting the classical procedure is that the complementation of attractor sets would break the invariant of downward-closedness on which the antichain representation relies. We overcome this difficulty by decomposing problem instances recursively into games with a combination of reachability, safety, and simpler parity conditions. We also report on an experimental implementation of our algorithm: to our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs.},
author = {Berwanger, Dietmar and Chatterjee, Krishnendu and De Wulf, Martin and Doyen, Laurent and Henzinger, Thomas A},
journal = {Information and Computation},
number = {10},
pages = {1206 -- 1220},
publisher = {Elsevier},
title = {{Strategy construction for parity games with imperfect information}},
doi = {10.1016/j.ic.2009.09.006},
volume = {208},
year = {2010},
}
@inproceedings{3864,
abstract = {Often one has a preference order among the different systems that satisfy a given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal-synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification tinder the given input assumption, synthesize a system that optimizes the measured value. For safety specifications and measures that are defined by mean-payoff automata, the optimal-synthesis problem amounts to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be done in polynomial time. For general omega-regular specifications, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. We present some experimental results showing optimal systems that were automatically generated in this way.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Singh, Rohit},
location = {Edinburgh, United Kingdom},
pages = {380 -- 395},
publisher = {Springer},
title = {{Measuring and synthesizing systems in probabilistic environments}},
doi = {10.1007/978-3-642-14295-6_34},
volume = {6174},
year = {2010},
}
@inproceedings{3866,
abstract = {Systems ought to behave reasonably even in circumstances that are not anticipated in their specifications. We propose a definition of robustness for liveness specifications which prescribes, for any number of environment assumptions that are violated, a minimal number of system guarantees that must still be fulfilled. This notion of robustness can be formulated and realized using a Generalized Reactivity formula. We present an algorithm for synthesizing robust systems from such formulas. For the important special case of Generalized Reactivity formulas of rank 1, our algorithm improves the complexity of [PPS06] for large specifications with a small number of assumptions and guarantees.},
author = {Bloem, Roderick and Chatterjee, Krishnendu and Greimel, Karin and Henzinger, Thomas A and Jobstmann, Barbara},
editor = {Touili, Tayssir and Cook, Byron and Jackson, Paul},
location = {Edinburgh, UK},
pages = {410 -- 424},
publisher = {Springer},
title = {{Robustness in the presence of liveness}},
doi = {10.1007/978-3-642-14295-6_36},
volume = {6174},
year = {2010},
}
@article{3867,
abstract = {Weighted automata are nondeterministic automata with numerical weights on transitions. They can define quantitative languages L that assign to each word w a real number L(w). In the case of infinite words, the value of a run is naturally computed as the maximum, limsup, liminf, limit-average, or discounted-sum of the transition weights. The value of a word w is the supremum of the values of the runs over w. We study expressiveness and closure questions about these quantitative languages. We first show that the set of words with value greater than a threshold can be omega-regular for deterministic limit-average and discounted-sum automata, while this set is always omega-regular when the threshold is isolated (i.e., some neighborhood around the threshold contains no word). In the latter case, we prove that the omega-regular language is robust against small perturbations of the transition weights. We next consider automata with transition weights 0 or 1 and show that they are as expressive as general weighted automata in the limit-average case, but not in the discounted-sum case. Third, for quantitative languages L-1 and L-2, we consider the operations max(L-1, L-2), min(L-1, L-2), and 1 - L-1, which generalize the boolean operations on languages, as well as the sum L-1 + L-2. We establish the closure properties of all classes of quantitative languages with respect to these four operations.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
journal = {Logical Methods in Computer Science},
number = {3},
pages = {1 -- 23},
publisher = {International Federation of Computational Logic},
title = {{Expressiveness and closure properties for quantitative languages}},
doi = {10.2168/LMCS-6(3:10)2010},
volume = {6},
year = {2010},
}
@article{3868,
abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative generalization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative mu-calculus and related probabilistic logics. We first show that the metrics provide a bound for the difference in long-run average and discounted average behavior across states, indicating that the metrics can be used both in system verification, and in performance evaluation. For turn-based games and MDPs, we provide a polynomial-time algorithm for the computation of the one-step metric distance between states. The algorithm is based on linear programming; it improves on the previous known exponential-time algorithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known algorithms for Markov chains. For the bisimulation kernel of the metric our algorithm works in time O(n(4)) for both turn-based games and MDPs; improving the previously best known O(n(9).log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance be tween states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be done via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(vertical bar G vertical bar(O(vertical bar G vertical bar 5))) time complexity, improving the previously known reduction, which yielded O(vertical bar G vertical bar(O(vertical bar G vertical bar 7))) time complexity. These algorithms can be iterated to approximate the metrics using binary search},
author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath},
journal = {Logical Methods in Computer Science},
number = {3},
pages = {1 -- 27},
publisher = {International Federation of Computational Logic},
title = {{Algorithms for game metrics}},
doi = {10.2168/LMCS-6(3:13)2010},
volume = {6},
year = {2010},
}
@article{3901,
abstract = {We are interested in 3-dimensional images given as arrays of voxels with intensity values. Extending these values to acontinuous function, we study the robustness of homology classes in its level and interlevel sets, that is, the amount of perturbationneeded to destroy these classes. The structure of the homology classes and their robustness, over all level and interlevel sets, can bevisualized by a triangular diagram of dots obtained by computing the extended persistence of the function. We give a fast hierarchicalalgorithm using the dual complexes of oct-tree approximations of the function. In addition, we show that for balanced oct-trees, thedual complexes are geometrically realized in $R^3$ and can thus be used to construct level and interlevel sets. We apply these tools tostudy 3-dimensional images of plant root systems.},
author = {Bendich, Paul and Edelsbrunner, Herbert and Kerber, Michael},
journal = {IEEE Transactions of Visualization and Computer Graphics},
number = {6},
pages = {1251 -- 1260},
publisher = {IEEE},
title = {{Computing robustness and persistence for images}},
doi = {10.1109/TVCG.2010.139},
volume = {16},
year = {2010},
}
@article{3904,
abstract = {Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by gen- etic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony.},
author = {Ugelvig, Line V and Kronauer, Daniel and Schrempf, Alexandra and Heinze, Jürgen and Cremer, Sylvia},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1695},
pages = {2821 -- 2828},
publisher = {Royal Society, The},
title = {{Rapid anti-pathogen response in ant societies relies on high genetic diversity}},
doi = {10.1098/rspb.2010.0644},
volume = {277},
year = {2010},
}
@article{3960,
abstract = {When lymphocytes follow chemotactic cues, they can adopt different migratory modes depending on the geometry and molecular composition of their extracellular environment. In this issue of The EMBO Journal, Klemke et al (2010) describe a novel Ras-dependent chemokine receptor signalling pathway that leads to activation of cofilin, which in turn amplifies actin turnover. This signalling module is exclusively required for lymphocyte migration in three-dimensional (3D) environments, but not for locomotion on two-dimensional (2D) surfaces.},
author = {Michele Weber and Michael Sixt},
journal = {EMBO Journal},
number = {17},
pages = {2861 -- 2863},
publisher = {Wiley-Blackwell},
title = {{MEK signalling tunes actin treadmilling for interstitial lymphocyte migration}},
doi = {10.1038/emboj.2010.183},
volume = {29},
year = {2010},
}
@article{4157,
abstract = {Integrin- and cadherin-mediated adhesion is central for cell and tissue morphogenesis, allowing cells and tissues to change shape without loosing integrity. Studies predominantly in cell culture showed that mechanosensation through adhesion structures is achieved by force-mediated modulation of their molecular composition. The specific molecular composition of adhesion sites in turn determines their signalling activity and dynamic reorganization. Here, we will review how adhesion sites respond to mecanical stimuli, and how spatially and temporally regulated signalling from different adhesion sites controls cell migration and tissue morphogenesis.},
author = {Papusheva, Ekaterina and Heisenberg, Carl-Philipp J},
journal = {EMBO Journal},
number = {16},
pages = {2753 -- 2768},
publisher = {Wiley-Blackwell},
title = {{Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis}},
doi = {10.1038/emboj.2010.182},
volume = {29},
year = {2010},
}
@article{4243,
abstract = {We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite number of individuals sampled uniformly at random (or more generally `far enough apart') from a two-dimensional torus of sidelength L as L tends to infinity. Under appropriate conditions (and on a suitable timescale) we can obtain as limiting genealogical processes a Kingman coalescent, a more general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local coalescence mechanism).},
author = {Barton, Nicholas H and Etheridge, Alison and Véber, Amandine},
journal = {Electronic Journal of Probability},
number = {7},
pages = {162 -- 216},
publisher = {Institute of Mathematical Statistics},
title = {{A new model for evolution in a spatial continuum}},
doi = {10.1214/EJP.v15-741},
volume = {15},
year = {2010},
}
@inbook{4339,
abstract = {Mit diesem Buch möchten wir einen Überblick der aktuellen Diskussion zum Thema Bibliothek 2.0 geben und den Stand der tatsächlichen Umsetzung der Web 2.0-Ansätze in deutschsprachigen Bibliotheken beleuchten. An dieser Stelle ist die Frage erlaubt, warum es zu einer Zeit, in der es bereits die ersten "Web 3.0"- Konferenzen gibt, eines Handbuches der Bibliothek 2.0 noch bedarf. Und warum es überhaupt ein deutschsprachiges Handbuch zur Bibliothek 2.0 braucht, wo es doch bereits verschiedenste Publikationen zu diesem Thema aus anderen Ländern, insbesondere des angloamerikanischen Raums gibt. Ist dazu nicht bereits alles gesagt?},
author = {Bergmann, Julia and Danowski, Patrick},
booktitle = {Handbuch Bibliothek 2.0},
editor = {Bergmann, Julia and Danowski, Patrick},
pages = {5 -- 20},
publisher = {De Gruyter},
title = {{Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch}},
doi = {10.1515/9783110232103},
year = {2010},
}
@misc{4340,
abstract = {More and more libraries starting semantic web projects. The question about the license of the data
is not discussed or the discussion is deferred to the end of project. in this paper is discussed why
the question of the license is so important in context of the semantic web that is should be one of the
first aspects in a semantic web project. Also it will be shown why a public domain weaver is the
only solution that fulfill the the special requirements of the semantic web and that guaranties the
reuseablitly of semantic library data for a sustainability of the projects. },
author = {Danowski, Patrick},
booktitle = {European Library Automation Group (ELAG) 2010},
publisher = {Elsevier},
title = {{Open bibliographic data}},
year = {2010},
}
@book{4346,
abstract = {With the term "Library 2.0" the editors mean an institution which applies the principles of the Web 2.0 such as openness, re-use, collaboration and interaction in the entire organization. Libraries are extending their service offerings and work processes to include the potential of Web 2.0 technologies. This changes the job description and self-image of librarians. The collective volume offers a complete overview of the topic Library 2.0 and the current state of developments from a technological, sociological, information theoretical and practice-oriented perspective.},
author = {Danowski, Patrick and Bergmann, Julia},
publisher = {De Gruyter},
title = {{Handbuch Bibliothek 2.0}},
year = {2010},
}
@inproceedings{4369,
abstract = {In this paper we propose a novel technique for constructing timed automata from properties expressed in the logic mtl, under bounded-variability assumptions. We handle full mtl and include all future operators. Our construction is based on separation of the continuous time monitoring of the input sequence and discrete predictions regarding the future. The separation of the continuous from the discrete allows us to determinize our automata in an exponential construction that does not increase the number of clocks. This leads to a doubly exponential construction from mtl to deterministic timed automata, compared with triply exponential using existing approaches. We offer an alternative to the existing approach to linear real-time model checking, which has never been implemented. It further offers a unified framework for model checking, runtime monitoring, and synthesis, in an approach that can reuse tools, implementations, and insights from the discrete setting.},
author = {Nickovic, Dejan and Piterman, Nir},
editor = {Henzinger, Thomas A. and Chatterjee, Krishnendu},
location = {Klosterneuburg, Austria},
pages = {152 -- 167},
publisher = {Springer},
title = {{From MTL to deterministic timed automata}},
doi = {10.1007/978-3-642-15297-9_13},
volume = {6246},
year = {2010},
}
@inproceedings{4378,
abstract = {Techniques such as verification condition generation, predicate abstraction, and expressive type systems reduce software verification to proving formulas in expressive logics. Programs and their specifications often make use of data structures such as sets, multisets, algebraic data types, or graphs. Consequently, formulas generated from verification also involve such data structures. To automate the proofs of such formulas we propose a logic (a “calculus”) of such data structures. We build the calculus by starting from decidable logics of individual data structures, and connecting them through functions and sets, in ways that go beyond the frameworks such as Nelson-Oppen. The result are new decidable logics that can simultaneously specify properties of different kinds of data structures and overcome the limitations of the individual logics. Several of our decidable logics include abstraction functions that map a data structure into its more abstract view (a tree into a multiset, a multiset into a set), into a numerical quantity (the size or the height), or into the truth value of a candidate data structure invariant (sortedness, or the heap property). For algebraic data types, we identify an asymptotic many-to-one condition on the abstraction function that guarantees the existence of a decision procedure. In addition to the combination based on abstraction functions, we can combine multiple data structure theories if they all reduce to the same data structure logic. As an instance of this approach, we describe a decidable logic whose formulas are propositional combinations of formulas in: weak monadic second-order logic of two successors, two-variable logic with counting, multiset algebra with Presburger arithmetic, the Bernays-Schönfinkel-Ramsey class of first-order logic, and the logic of algebraic data types with the set content function. The subformulas in this combination can share common variables that refer to sets of objects along with the common set algebra operations. Such sound and complete combination is possible because the relations on sets definable in the component logics are all expressible in Boolean Algebra with Presburger Arithmetic. Presburger arithmetic and its new extensions play an important role in our decidability results. In several cases, when we combine logics that belong to NP, we can prove the satisfiability for the combined logic is still in NP.},
author = {Kuncak, Viktor and Piskac, Ruzica and Suter, Philippe and Wies, Thomas},
editor = {Barthe, Gilles and Hermenegildo, Manuel},
location = {Madrid, Spain},
pages = {26 -- 44},
publisher = {Springer},
title = {{Building a calculus of data structures}},
doi = {10.1007/978-3-642-11319-2_6},
volume = {5944},
year = {2010},
}
@article{4379,
abstract = {The formal specification component of verification can be exported to simulation through the idea of property checkers. The essence of this approach is the automatic construction of an observer from the specification in the form of a program that can be interfaced with a simulator and alert the user if the property is violated by a simulation trace. Although not complete, this lighter approach to formal verification has been effectively used in software and digital hardware to detect errors. Recently, the idea of property checkers has been extended to analog and mixed-signal systems.
In this paper, we apply the property-based checking methodology to an industrial and realistic example of a DDR2 memory interface. The properties describing the DDR2 analog behavior are expressed in the formal specification language stl/psl in form of assertions. The simulation traces generated from an actual DDR2 interface design are checked with respect to the stl/psl assertions using the amt tool. The focus of this paper is on the translation of the official (informal and descriptive) specification of two non-trivial DDR2 properties into stl/psl assertions. We study both the benefits and the current limits of such approach.
},
author = {Jones, Kevin D and Konrad,Victor and Dejan Nickovic},
journal = {Formal Methods in System Design},
number = {2},
pages = {114 -- 130},
publisher = {Springer},
title = {{Analog property checkers: a DDR2 case study}},
doi = {10.1007/s10703-009-0085-x},
volume = {36},
year = {2010},
}
@inproceedings{4380,
abstract = {Cloud computing is an emerging paradigm aimed to offer users pay-per-use computing resources, while leaving the burden of managing the computing infrastructure to the cloud provider. We present a new programming and pricing model that gives the cloud user the flexibility of trading execution speed and price on a per-job basis. We discuss the scheduling and resource management challenges for the cloud provider that arise in the implementation of this model. We argue that techniques from real-time and embedded software can be useful in this context.},
author = {Henzinger, Thomas A and Tomar, Anmol and Singh, Vasu and Wies, Thomas and Zufferey, Damien},
location = {Arizona, USA},
pages = {1 -- 8},
publisher = {ACM},
title = {{A marketplace for cloud resources}},
doi = {10.1145/1879021.1879022},
year = {2010},
}
@inproceedings{4381,
abstract = {Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We claim that, in order to realize the full potential of cloud computing, the user must be presented with a pricing model that offers flexibility at the requirements level, such as a choice between different degrees of execution speed and the cloud provider must be presented with a programming model that offers flexibility at the execution level, such as a choice between different scheduling policies. In such a flexible framework, with each job, the user purchases a virtual computer with the desired speed and cost characteristics, and the cloud provider can optimize the utilization of resources across a stream of jobs from different users. We designed a flexible framework to test our hypothesis, which is called FlexPRICE (Flexible Provisioning of Resources in a Cloud Environment) and works as follows. A user presents a job to the cloud. The cloud finds different schedules to execute the job and presents a set of quotes to the user in terms of price and duration for the execution. The user then chooses a particular quote and the cloud is obliged to execute the job according to the chosen quote. FlexPRICE thus hides the complexity of the actual scheduling decisions from the user, but still provides enough flexibility to meet the users actual demands. We implemented FlexPRICE in a simulator called PRICES that allows us to experiment with our framework. We observe that FlexPRICE provides a wide range of execution options-from fast and expensive to slow and cheap-- for the whole spectrum of data-intensive and computation-intensive jobs. We also observe that the set of quotes computed by FlexPRICE do not vary as the number of simultaneous jobs increases.},
author = {Henzinger, Thomas A and Tomar, Anmol and Singh, Vasu and Wies, Thomas and Zufferey, Damien},
location = {Miami, USA},
pages = {83 -- 90},
publisher = {IEEE},
title = {{FlexPRICE: Flexible provisioning of resources in a cloud environment}},
doi = {10.1109/CLOUD.2010.71},
year = {2010},
}
@inproceedings{4382,
abstract = {Transactional memory (TM) has shown potential to simplify the task of writing concurrent programs. Inspired by classical work on databases, formal definitions of the semantics of TM executions have been proposed. Many of these definitions assumed that accesses to shared data are solely performed through transactions. In practice, due to legacy code and concurrency libraries, transactions in a TM have to share data with non-transactional operations. The semantics of such interaction, while widely discussed by practitioners, lacks a clear formal specification. Those interactions can vary, sometimes in subtle ways, between TM implementations and underlying memory models. We propose a correctness condition for TMs, parametrized opacity, to formally capture the now folklore notion of strong atomicity by stipulating the two following intuitive requirements: first, every transaction appears as if it is executed instantaneously with respect to other transactions and non-transactional operations, and second, non-transactional operations conform to the given underlying memory model. We investigate the inherent cost of implementing parametrized opacity. We first prove that parametrized opacity requires either instrumenting non-transactional operations (for most memory models) or writing to memory by transactions using potentially expensive read-modify-write instructions (such as compare-and-swap). Then, we show that for a class of practical relaxed memory models, parametrized opacity can indeed be implemented with constant-time instrumentation of non-transactional writes and no instrumentation of non-transactional reads. We show that, in practice, parametrizing the notion of correctness allows developing more efficient TM implementations.},
author = {Guerraoui, Rachid and Henzinger, Thomas A and Kapalka, Michal and Singh, Vasu},
location = {Santorini, Greece},
pages = {263 -- 272},
publisher = {ACM},
title = {{Transactions in the jungle}},
doi = {10.1145/1810479.1810529},
year = {2010},
}
@inproceedings{4388,
abstract = {GIST is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides the first and efficient implementations of several reduction-based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Radhakrishna, Arjun},
location = {Edinburgh, UK},
pages = {665 -- 669},
publisher = {Springer},
title = {{GIST: A solver for probabilistic games}},
doi = {10.1007/978-3-642-14295-6_57},
volume = {6174},
year = {2010},
}
@inproceedings{4389,
abstract = {Digital components play a central role in the design of complex embedded systems. These components are interconnected with other, possibly analog, devices and the physical environment. This environment cannot be entirely captured and can provide inaccurate input data to the component. It is thus important for digital components to have a robust behavior, i.e. the presence of a small change in the input sequences should not result in a drastic change in the output sequences. In this paper, we study a notion of robustness for sequential circuits. However, since sequential circuits may have parts that are naturally discontinuous (e.g., digital controllers with switching behavior), we need a flexible framework that accommodates this fact and leaves discontinuous parts of the circuit out from the robustness analysis. As a consequence, we consider sequential circuits that have their input variables partitioned into two disjoint sets: control and disturbance variables. Our contributions are (1) a definition of robustness for sequential circuits as a form of continuity with respect to disturbance variables, (2) the characterization of the exact class of sequential circuits that are robust according to our definition, (3) an algorithm to decide whether a sequential circuit is robust or not.},
author = {Doyen, Laurent and Henzinger, Thomas A and Legay, Axel and Nickovic, Dejan},
pages = {77 -- 84},
publisher = {IEEE},
title = {{Robustness of sequential circuits}},
doi = {10.1109/ACSD.2010.26},
year = {2010},
}
@inproceedings{4390,
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 vertex stores 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 implementation and proved that the corrected version is linearizable.},
author = {Cerny, Pavol and Radhakrishna, Arjun and Zufferey, Damien and Chaudhuri, Swarat and Alur, Rajeev},
location = {Edinburgh, UK},
pages = {465 -- 479},
publisher = {Springer},
title = {{Model checking of linearizability of concurrent list implementations}},
doi = {10.1007/978-3-642-14295-6_41},
volume = {6174},
year = {2010},
}
@inproceedings{4393,
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 implementation 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},
location = {Paris, France},
pages = {235 -- 268},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Simulation distances}},
doi = {10.1007/978-3-642-15375-4_18},
volume = {6269},
year = {2010},
}
@inproceedings{4396,
abstract = {Shape analysis is a promising technique to prove program properties about recursive data structures. The challenge is to automatically determine the data-structure type, and to supply the shape analysis with the necessary information about the data structure. We present a stepwise approach to the selection of instrumentation predicates for a TVLA-based shape analysis, which takes us a step closer towards the fully automatic verification of data structures. The approach uses two techniques to guide the refinement of shape abstractions: (1) during program exploration, an explicit heap analysis collects sample instances of the heap structures, which are used to identify the data structures that are manipulated by the program; and (2) during abstraction refinement along an infeasible error path, we consider different possible heap abstractions and choose the coarsest one that eliminates the infeasible path. We have implemented this combined approach for automatic shape refinement as an extension of the software model checker BLAST. Example programs from a data-structure library that manipulate doubly-linked lists and trees were successfully verified by our tool.},
author = {Beyer, Dirk and Henzinger, Thomas A and Théoduloz, Grégory and Zufferey, Damien},
editor = {Rosenblum, David and Taenzer, Gabriele},
location = {Paphos, Cyprus},
pages = {263 -- 277},
publisher = {Springer},
title = {{Shape refinement through explicit heap analysis}},
doi = {10.1007/978-3-642-12029-9_19},
volume = {6013},
year = {2010},
}
@inproceedings{2980,
abstract = {Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic
building blocks of many practical cryptographic applications such as
identification schemes, group signatures, and secure multi-party
computation (SMPC). Currently, first applications that essentially
rely on ZK-PoKs are being deployed in the real world. The most
prominent example is the Direct Anonymous Attestation (DAA)
protocol, which was adopted by the Trusted Computing Group (TCG)
and implemented as one of the functionalities of the cryptographic
chip Trusted Platform Module (TPM).
Implementing systems using ZK-PoK turns out to be challenging,
since ZK-PoK are significantly more complex than standard crypto
primitives (e.g., encryption and signature schemes). As a result,
the design-implementation cycles of ZK-PoK are time-consuming
and error-prone.
To overcome this, we present a compiler with corresponding languages
for the automatic generation of sound and efficient ZK-PoK based on
Σ-protocols. The protocol designer using our compiler formulates
the goal of a ZK-PoK proof in a high-level protocol specification language,
which abstracts away unnecessary technicalities from the designer. The
compiler then automatically generates the protocol implementation in
Java code; alternatively, the compiler can output a description of the
protocol in LaTeX which can be used for documentation or verification.},
author = {Bangerter, Endre and Briner, Thomas and Henecka, Wilko and Stephan Krenn and Sadeghi, Ahmad-Reza and Schneider, Thomas},
editor = {Martinelli, Fabio and Preneel, Bart},
pages = {67 -- 82},
publisher = {Springer},
title = {{Automatic Generation of Sigma-Protocols}},
doi = {10.1007/978-3-642-16441-5},
volume = {6391},
year = {2010},
}
@article{3072,
abstract = {Development of plants and their adaptive capacity towards ever‐changing environmental conditions largely depend on the spatial distribution of the plant hormone auxin. At the cellular level, various internal and external signals are translated into specific changes in the polar, subcellular localization of auxin transporters from the PIN family thereby directing and redirecting the intercellular fluxes of auxin. The current model of polar targeting of PIN proteins towards different plasma membrane domains encompasses apolar secretion of newly synthesized PINs followed by endocytosis and recycling back to the plasma membrane in a polarized manner. In this review, we follow the subcellular march of the PINs and highlight the cellular and molecular mechanisms behind polar foraging and subcellular trafficking pathways. Also, the entry points for different signals and regulations including by auxin itself will be discussed within the context of morphological and developmental consequences of polar targeting and subcellular trafficking.},
author = {Grunewald, Wim and Friml, Jirí},
journal = {EMBO Journal},
number = {16},
pages = {2700 -- 2714},
publisher = {Wiley-Blackwell},
title = {{The march of the PINs: Developmental plasticity by dynamic polar targeting in plant cells}},
doi = {10.1038/emboj.2010.181},
volume = {29},
year = {2010},
}
@article{3077,
author = {Friml, Jirí and Jones, Angharad},
journal = {Plant Physiology},
number = {2},
pages = {458 -- 462},
publisher = {American Society of Plant Biologists},
title = {{Endoplasmic reticulum: The rising compartment in auxin biology}},
doi = {10.1104/pp.110.161380},
volume = {154},
year = {2010},
}
@article{3303,
abstract = {Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. },
author = {Weissman, Daniel and Feldman, Marcus and Fisher, Daniel},
journal = {Genetics},
number = {4},
pages = {1389 -- 1410},
publisher = {Genetics Society of America},
title = {{The rate of fitness-valley crossing in sexual populations}},
doi = {10.1534/genetics.110.123240},
volume = {186},
year = {2010},
}
@article{3306,
abstract = {We use methods from combinatorics and algebraic statistics to study analogues of birth-and-death processes that have as their state space a finite subset of the m-dimensional lattice and for which the m matrices that record the transition probabilities in each of the lattice directions commute pairwise. One reason such processes are of interest is that the transition matrix is straightforward to diagonalize, and hence it is easy to compute n step transition probabilities. The set of commuting birth-and-death processes decomposes as a union of toric varieties, with the main component being the closure of all processes whose nearest neighbor transition probabilities are positive. We exhibit an explicit monomial parametrization for this main component, and we explore the boundary components using primary decomposition.},
author = {Evans, Steven N and Sturmfels, Bernd and Caroline Uhler},
journal = {The Annals of Applied Probability},
pages = {238 -- 266},
publisher = {Institute of Mathematical Statistics},
title = {{Commuting birth and death processes}},
doi = {10.1214/09-AAP615},
volume = {20},
year = {2010},
}
@article{3308,
abstract = {We study multivariate normal models that are described by linear constraints on the inverse of the covariance matrix. Maximum likelihood estimation for such models leads to the problem of maximizing the determinant function over a spectrahedron, and to the problem of characterizing the image of the positive definite cone under an arbitrary linear projection. These problems at the interface of statistics and optimization are here examined from the perspective of convex algebraic geometry.},
author = {Sturmfels, Bernd and Caroline Uhler},
journal = {Annals of the Institute of Statistical Mathematics},
number = {4},
pages = {603 -- 638},
publisher = {Springer},
title = {{Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry}},
doi = {10.1007/s10463-010-0295-4},
volume = {62},
year = {2010},
}
@inproceedings{3430,
abstract = {These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.},
author = {Gasper Tkacik},
publisher = {Elsevier},
title = {{Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics}},
year = {2010},
}
@article{3538,
abstract = {How seizures start is a major question in epilepsy research. Preictal EEG changes occur in both human patients and animal models, but their underlying mechanisms and relationship with seizure initiation remain unknown. Here we demonstrate the existence, in the hippocampal CA1 region, of a preictal state characterized by the progressive and global increase in neuronal activity associated with a widespread buildup of low-amplitude high-frequency activity (HFA) (> 100 Hz) and reduction in system complexity. HFA is generated by the firing of neurons, mainly pyramidal cells, at much lower frequencies. Individual cycles of HFA are generated by the near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization; the presence of very similar HFA in the high-potassium model shows that it does not depend on an absence of synaptic transmission. Immediately before seizure onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing perturbations can trigger seizures. Transition to seizure is characterized by a rapid expansion and fusion of the neuronal populations responsible for HFA, associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous cluster generating the high-amplitude low-frequency activity of the seizure.},
author = {Jiruska, Premysl and Csicsvari, Jozsef L and Powell, Andrew and Fox, John and Chang, Wei and Vreugdenhil, Martin and Li, Xiaoli and Palus, Milan and Bujan, Alejandro and Dearden, Richard and Jefferys, John},
journal = {Journal of Neuroscience},
number = {16},
pages = {5690 -- 5701},
publisher = {Society for Neuroscience},
title = {{High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro}},
doi = {10.1523/JNEUROSCI.0535-10.2010},
volume = {30},
year = {2010},
}
@inproceedings{4361,
abstract = {Depth-bounded processes form the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. In this paper we develop an adequate domain of limits for the well-structured transition systems that are induced by depth-bounded processes. An immediate consequence of our result is that there exists a forward algorithm that decides the covering problem for this class. Unlike backward algorithms, the forward algorithm terminates even if the depth of the process is not known a priori. More importantly, our result suggests a whole spectrum of forward algorithms that enable the effective verification of a large class of mobile systems.},
author = {Wies, Thomas and Zufferey, Damien and Henzinger, Thomas A},
editor = {Ong, Luke},
location = {Paphos, Cyprus},
pages = {94 -- 108},
publisher = {Springer},
title = {{Forward analysis of depth-bounded processes}},
doi = {10.1007/978-3-642-12032-9_8},
volume = {6014},
year = {2010},
}
@article{9485,
abstract = {Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.},
author = {Zemach, Assaf and Kim, M. Yvonne and Silva, Pedro and Rodrigues, Jessica A. and Dotson, Bradley and Brooks, Matthew D. and ZILBERMAN, Daniel},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences},
number = {43},
pages = {18729--18734},
publisher = {National Academy of Sciences},
title = {{Local DNA hypomethylation activates genes in rice endosperm}},
doi = {10.1073/pnas.1009695107},
volume = {107},
year = {2010},
}
@article{9489,
abstract = {Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.},
author = {Zemach, Assaf and ZILBERMAN, Daniel},
issn = {1879-0445},
journal = {Current Biology},
number = {17},
pages = {R780--R785},
publisher = {Elsevier},
title = {{Evolution of eukaryotic DNA methylation and the pursuit of safer sex}},
doi = {10.1016/j.cub.2010.07.007},
volume = {20},
year = {2010},
}
@article{228,
abstract = {Let X be a projective non-singular quartic hypersurface of dimension 39 or more, which is defined over . We show that X() is non-empty provided that X() is non-empty and X has p-adic points for every prime p.},
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Journal fur die Reine und Angewandte Mathematik},
number = {629},
pages = {37 -- 88},
publisher = {Walter de Gruyter},
title = {{Rational points on quartic hypersurfaces}},
doi = {10.1515/CRELLE.2009.026},
year = {2009},
}
@article{229,
abstract = {An upper bound of the expected order of magnitude is established for the number of ℚ-rational points of bounded height on Châtelet surfaces defined over ℚ.},
author = {Timothy Browning},
journal = {Mathematische Annalen},
number = {1},
pages = {41 -- 50},
publisher = {Springer Nature},
title = {{Linear growth for Châtelet surfaces}},
doi = {10.1007/s00208-009-0383-z},
volume = {346},
year = {2009},
}
@article{2384,
abstract = {We prove the Lee-Huang-Yang formula for the ground state energy of the 3D Bose gas with repulsive interactions described by the exponential function, in a simultaneous limit of weak coupling and high density. In particular, we show that the Bogoliubov approximation is exact in an appropriate parameter regime, as far as the ground state energy is concerned.},
author = {Giuliani, Alessandro and Robert Seiringer},
journal = {Journal of Statistical Physics},
number = {5-6},
pages = {915 -- 934},
publisher = {Springer},
title = {{The ground state energy of the weakly interacting Bose gas at high density}},
doi = {10.1007/s10955-009-9718-0},
volume = {135},
year = {2009},
}
@article{2385,
abstract = {We consider an ultracold rotating Bose gas in a harmonic trap close to the critical angular velocity, so that the system can be considered to be confined to the lowest Landau level. With this assumption we prove that the Gross-Pitaevskii energy functional accurately describes the ground-state energy of the corresponding N -body Hamiltonian with contact interaction provided the total angular momentum L is much less than N2. While the Gross-Pitaevskii energy is always an obvious variational upper bound to the ground-state energy, a more refined analysis is needed to establish it as an exact lower bound. We also discuss the question of Bose-Einstein condensation in the parameter range considered. Coherent states together with inequalities in spaces of analytic functions are the main technical tools.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {6},
publisher = {American Physical Society},
title = {{Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime}},
doi = {10.1103/PhysRevA.79.063626},
volume = {79},
year = {2009},
}
@article{2386,
abstract = {We prove exponential decay of the off-diagonal correlation function in the two-dimensional homogeneous Bose gas when a2 ρ is small and the temperature T satisfies T> 4πρ ln | ln (a2 ρ) |. Here, a is the scattering length of the repulsive interaction potential and ρ is the density. To the leading order in a2 ρ, this bound agrees with the expected critical temperature for superfluidity. In the three-dimensional Bose gas, exponential decay is proved when T- Tc (0) Tc (0) >5 a ρ1/3, where Tc (0) is the critical temperature of the ideal gas. While this condition is not expected to be sharp, it gives a rigorous upper bound on the critical temperature for Bose-Einstein condensation.},
author = {Robert Seiringer and Ueltschi, Daniel},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {1},
publisher = {American Physical Society},
title = {{Rigorous upper bound on the critical temperature of dilute Bose gases}},
doi = {10.1103/PhysRevB.80.014502},
volume = {80},
year = {2009},
}
@article{2387,
abstract = {We consider a system of trapped spinless bosons interacting with a repulsive potential and subject to rotation. In the limit of rapid rotation and small scattering length, we rigorously show that the ground state energy converges to that of a simplified model Hamiltonian with contact interaction projected onto the Lowest Landau Level. This effective Hamiltonian models the bosonic analogue of the Fractional Quantum Hall Effect (FQHE). For a fixed number of particles, we also prove convergence of states; in particular, in a certain regime we show convergence towards the bosonic Laughlin wavefunction. This is the first rigorous justification of the effective FQHE Hamiltonian for rapidly rotating Bose gases. We review previous results on this effective Hamiltonian and outline open problems.},
author = {Lewin, Mathieu and Robert Seiringer},
journal = {Journal of Statistical Physics},
number = {5},
pages = {1040 -- 1062},
publisher = {Springer},
title = {{Strongly correlated phases in rapidly rotating Bose gases}},
doi = {10.1007/s10955-009-9833-y},
volume = {137},
year = {2009},
}