@inproceedings{3968,
abstract = {We describe an algorithm for segmenting three-dimensional medical imaging data modeled as a continuous function on a 3-manifold. It is related to watershed algorithms developed in image processing but is closer to its mathematical roots, which are Morse theory and homological algebra. It allows for the implicit treatment of an underlying mesh, thus combining the structural integrity of its mathematical foundations with the computational efficiency of image processing.},
author = {Edelsbrunner, Herbert and Harer, John},
location = {Zermatt, Switzerland},
pages = {36 -- 50},
publisher = {Springer},
title = {{The persistent Morse complex segmentation of a 3-manifold}},
doi = {10.1007/978-3-642-10470-1_4},
volume = {5903},
year = {2009},
}
@article{4136,
abstract = {Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation.},
author = {Polechova, Jitka and Barton, Nicholas H and Marion, Glenn},
journal = {American Naturalist},
number = {5},
pages = {E186 -- E204},
publisher = {University of Chicago Press},
title = {{Species' range: Adaptation in space and time}},
doi = {10.1086/605958},
volume = {174},
year = {2009},
}
@article{4242,
abstract = {Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.},
author = {Barton, Nicholas H and De Cara, Maria},
journal = {Evolution; International Journal of Organic Evolution},
number = {5},
pages = {1171 -- 1190},
publisher = {Wiley},
title = {{The evolution of strong reproductive isolation}},
doi = {10.1111/j.1558-5646.2009.00622.x},
volume = {63},
year = {2009},
}
@inproceedings{4383,
abstract = {Pseudo-code descriptions of STMs assume sequentially consistent program execution and atomicity of high-level STM operations like read, write, and commit. These assumptions are often violated in realistic settings, as STM implementations run on relaxed memory models, with the atomicity of operations as provided by the hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We present RML, a new high-level language for expressing concurrent algorithms with a hardware-level atomicity of instructions, and whose semantics is parametrized by various relaxed memory models. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order.},
author = {Guerraoui, Rachid and Thomas Henzinger and Vasu Singh},
pages = {321 -- 336},
publisher = {Springer},
title = {{Software transactional memory on relaxed memory models}},
doi = {10.1007/978-3-642-02658-4_26},
volume = {5643},
year = {2009},
}
@inproceedings{4403,
abstract = {For programs whose data variables range over boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this paper, we consider algorithmic verification of programs that use boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over a potentially unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) Pspace-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly-nested loops. The second result establishes connections to automata and logics defining languages over data words.},
author = {Alur, Rajeev and Cerny, Pavol and Weinstein, Scott},
location = {Coimbra, Portugal},
pages = {86 -- 101},
publisher = {Springer},
title = {{Algorithmic analysis of array-accessing programs}},
doi = {10.1007/978-3-642-04027-6_9},
volume = {5771},
year = {2009},
}
@inproceedings{4453,
abstract = {We present an on-the-fly abstraction technique for infinite-state continuous -time Markov chains. We consider Markov chains that are specified by a finite set of transition classes. Such models naturally represent biochemical reactions and therefore play an important role in the stochastic modeling of biological systems. We approximate the transient probability distributions at various time instances by solving a sequence of dynamically constructed abstract models, each depending on the previous one. Each abstract model is a finite Markov chain that represents the behavior of the original, infinite chain during a specific time interval. Our approach provides complete information about probability distributions, not just about individual parameters like the mean. The error of each abstraction can be computed, and the precision of the abstraction refined when desired. We implemented the algorithm and demonstrate its usefulness and efficiency on several case studies from systems biology.},
author = {Thomas Henzinger and Maria Mateescu and Wolf, Verena},
pages = {337 -- 352},
publisher = {Springer},
title = {{Sliding-window abstraction for infinite Markov chains}},
doi = {10.1007/978-3-642-02658-4_27},
volume = {5643},
year = {2009},
}
@inproceedings{4542,
abstract = {Weighted automata are finite automata with numerical weights on transitions. Nondeterministic weighted automata define quantitative languages L that assign to each word w a real number L(w) computed as the maximal value of all runs over w, and the value of a run r is a function of the sequence of weights that appear along r. There are several natural functions to consider such as Sup, LimSup, LimInf, limit average, and discounted sum of transition weights.
We introduce alternating weighted automata in which the transitions of the runs are chosen by two players in a turn-based fashion. Each word is assigned the maximal value of a run that the first player can enforce regardless of the choices made by the second player. We survey the results about closure properties, expressiveness, and decision problems for nondeterministic weighted automata, and we extend these results to alternating weighted automata.
For quantitative languages L 1 and L 2, we consider the pointwise operations max(L 1,L 2), min(L 1,L 2), 1 − L 1, and the sum L 1 + L 2. We establish the closure properties of all classes of alternating weighted automata with respect to these four operations.
We next compare the expressive power of the various classes of alternating and nondeterministic weighted automata over infinite words. In particular, for limit average and discounted sum, we show that alternation brings more expressive power than nondeterminism.
Finally, we present decidability results and open questions for the quantitative extension of the classical decision problems in automata theory: emptiness, universality, language inclusion, and language equivalence.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
location = {Wroclaw, Poland},
pages = {3 -- 13},
publisher = {Springer},
title = {{Alternating weighted automata}},
doi = {10.1007/978-3-642-03409-1_2},
volume = {5699},
year = {2009},
}
@inproceedings{4544,
abstract = {We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. We present in this paper a strategy improvement algorithm for computing the value of a concurrent safety game, that is, the maximal probability with which player 1 can enforce the safety objective. The algorithm yields a sequence of player-1 strategies which ensure probabilities of winning that converge monotonically to the value of the safety game. Our result is significant because the strategy improvement algorithm provides, for the first time, a way to approximate the value of a concurrent safety game from below. Since a value iteration algorithm, or a strategy improvement algorithm for reachability games, can be used to approximate the same value from above, the combination of both algorithms yields a method for computing a converging sequence of upper and lower bounds for the values of concurrent reachability and safety games. Previous methods could approximate the values of these games only from one direction, and as no rates of convergence are known, they did not provide a practical way to solve these games.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger},
pages = {197 -- 206},
publisher = {SIAM},
title = {{Termination criteria for solving concurrent safety and reachability games}},
doi = {10.1137/1.9781611973068.23},
year = {2009},
}
@inproceedings{4545,
abstract = {A stochastic game is a two-player game played oil a graph, where in each state the successor is chosen either by One of the players, or according to a probability distribution. We Survey Stochastic games with limsup and liminf objectives. A real-valued re-ward is assigned to each state, and the value of all infinite path is the limsup (resp. liminf) of all rewards along the path. The value of a stochastic game is the maximal expected value of an infinite path that call he achieved by resolving the decisions of the first player. We present the complexity of computing values of Stochastic games and their subclasses, and the complexity, of optimal strategies in such games. },
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
location = {Rhodos, Greece},
pages = {1 -- 15},
publisher = {Springer},
title = {{A survey of stochastic games with limsup and liminf objectives}},
doi = {10.1007/978-3-642-02930-1_1},
volume = {5556},
year = {2009},
}
@inproceedings{4569,
abstract = {Most specification languages express only qualitative constraints. However, among two implementations that satisfy a given specification, one may be preferred to another. For example, if a specification asks that every request is followed by a response, one may prefer an implementation that generates responses quickly but does not generate unnecessary responses. We use quantitative properties to measure the “goodness” of an implementation. Using games with corresponding quantitative objectives, we can synthesize “optimal” implementations, which are preferred among the set of possible implementations that satisfy a given specification.
In particular, we show how automata with lexicographic mean-payoff conditions can be used to express many interesting quantitative properties for reactive systems. In this framework, the synthesis of optimal implementations requires the solution of lexicographic mean-payoff games (for safety requirements), and the solution of games with both lexicographic mean-payoff and parity objectives (for liveness requirements). We present algorithms for solving both kinds of novel graph games.},
author = {Bloem, Roderick and Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara},
location = {Grenoble, France},
pages = {140 -- 156},
publisher = {Springer},
title = {{Better quality in synthesis through quantitative objectives}},
doi = {10.1007/978-3-642-02658-4_14},
volume = {5643},
year = {2009},
}
@inproceedings{4580,
abstract = {Alpaga is a solver for two-player parity games with imperfect information. Given the description of a game, it determines whether the first player can ensure to win and, if so, it constructs a winning strategy. The tool provides a symbolic implementation of a recent algorithm based on antichains.},
author = {Berwanger, Dietmar and Krishnendu Chatterjee and De Wulf, Martin and Doyen, Laurent and Thomas Henzinger},
pages = {58 -- 61},
publisher = {Springer},
title = {{Alpaga: A tool for solving parity games with imperfect information}},
doi = {10.1007/978-3-642-00768-2_7},
volume = {5505},
year = {2009},
}
@article{3051,
author = {Weijers, Dolf and Friml, Jirí},
journal = {Cell},
number = {6},
pages = {1172 -- 1172},
publisher = {Cell Press},
title = {{SnapShot: Auxin signaling and transport}},
doi = {10.1016/j.cell.2009.03.009},
volume = {136},
year = {2009},
}
@article{3052,
abstract = {The dynamic, differential distribution of the hormone auxin within plant tissues controls an impressive variety of developmental processes, which tailor plant growth and morphology to environmental conditions. Various environmental and endogenous signals can be integrated into changes in auxin distribution through their effects on local auxin biosynthesis and intercellular auxin transport. Individual cells interpret auxin largely by a nuclear signaling pathway that involves the F box protein TIR1 acting as an auxin receptor. Auxin-dependent TIR1 activity leads to ubiquitination-based degradation of transcriptional repressors and complex transcriptional reprogramming. Thus, auxin appears to be a versatile trigger of preprogrammed developmental changes in plant cells.},
author = {Vanneste, Steffen and Friml, Jirí},
journal = {Cell},
number = {6},
pages = {1005 -- 1016},
publisher = {Cell Press},
title = {{Auxin: A trigger for change in plant development}},
doi = {10.1016/j.cell.2009.03.001},
volume = {136},
year = {2009},
}
@article{3057,
abstract = {The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli.},
author = {Petrášek, Jan and Friml, Jirí},
journal = {Development},
number = {16},
pages = {2675 -- 2688},
publisher = {Company of Biologists},
title = {{Auxin transport routes in plant development}},
doi = {10.1242/dev.030353},
volume = {136},
year = {2009},
}
@article{3061,
abstract = {The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies.},
author = {Křeček, Pavel and Skůpa, Petr and Libus, Jiří and Naramoto, Satoshi and Tejos, Ricardo and Friml, Jirí and Zažímalová, Eva},
journal = {Genome Biology},
number = {12},
publisher = {BioMed Central},
title = {{The PIN-FORMED (PIN) protein family of auxin transporters}},
doi = {10.1186/gb-2009-10-12-249},
volume = {10},
year = {2009},
}
@article{3197,
abstract = {The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.
We show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.},
author = {Kumar, M Pawan and Vladimir Kolmogorov and Torr, Philip H},
journal = {Journal of Machine Learning Research},
pages = {71 -- 106},
publisher = {Microtome Publishing},
title = {{An analysis of convex relaxations for MAP estimation of discrete MRFs}},
volume = {10},
year = {2009},
}
@inproceedings{3503,
abstract = {We give polynomial-time algorithms for computing the values of Markov decision processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned to each state, and the value of an infinite path in the MDP is the limsup (resp. liminf) of all rewards along the path. The value of an MDP is the maximal expected value of an infinite path that can be achieved by resolving the decisions of the MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup and liminf objectives can be solved in NP ∩ coNP. },
author = {Krishnendu Chatterjee and Thomas Henzinger},
pages = {32 -- 45},
publisher = {Springer},
title = {{Probabilistic systems with limsup and liminf objectives}},
doi = {10.1007/978-3-642-03092-5_4},
volume = {5489},
year = {2009},
}
@inproceedings{2331,
abstract = {We present a review of recent work on the mathematical aspects of the BCS gap equation, covering our results of Ref. 9 as well our recent joint work with Hamza and Solovej and with Frank and Naboko, respectively. In addition, we mention some related new results.},
author = {Hainzl, Christian and Robert Seiringer},
pages = {117 -- 136},
publisher = {World Scientific Publishing},
title = {{ Spectral properties of the BCS gap equation of superfluidity}},
doi = {10.1142/9789812832382_0009},
year = {2008},
}
@inproceedings{2332,
abstract = {We present a rigorous proof of the appearance of quantized vortices in dilute trapped Bose gases with repulsive two-body interactions subject to rotation, which was obtained recently in joint work with Elliott Lieb.14 Starting from the many-body Schrödinger equation, we show that the ground state of such gases is, in a suitable limit, well described by the nonlinear Gross-Pitaevskii equation. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state.},
author = {Robert Seiringer},
pages = {241 -- 254},
publisher = {World Scientific Publishing},
title = {{Vortices and Spontaneous Symmetry Breaking in Rotating Bose Gases}},
doi = {10.1142/9789812832382_0017},
year = {2008},
}
@article{2374,
abstract = {A lower bound is derived on the free energy (per unit volume) of a homogeneous Bose gas at density Q and temperature T. In the dilute regime, i.e., when a3 1, where a denotes the scattering length of the pair-interaction potential, our bound differs to leading order from the expression for non-interacting particles by the term 4πa(2 2}-[ - c]2+). Here, c(T) denotes the critical density for Bose-Einstein condensation (for the non-interacting gas), and [ · ]+ = max{ ·, 0} denotes the positive part. Our bound is uniform in the temperature up to temperatures of the order of the critical temperature, i.e., T ~ 2/3 or smaller. One of the key ingredients in the proof is the use of coherent states to extend the method introduced in [17] for estimating correlations to temperatures below the critical one.},
author = {Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {3},
pages = {595 -- 636},
publisher = {Springer},
title = {{Free energy of a dilute Bose gas: Lower bound}},
doi = {10.1007/s00220-008-0428-2},
volume = {279},
year = {2008},
}
@article{2376,
abstract = {We derive upper and lower bounds on the critical temperature Tc and the energy gap Ξ (at zero temperature) for the BCS gap equation, describing spin- 1 2 fermions interacting via a local two-body interaction potential λV(x). At weak coupling λ 1 and under appropriate assumptions on V(x), our bounds show that Tc ∼A exp(-B/λ) and Ξ∼C exp(-B/λ) for some explicit coefficients A, B, and C depending on the interaction V(x) and the chemical potential μ. The ratio A/C turns out to be a universal constant, independent of both V(x) and μ. Our analysis is valid for any μ; for small μ, or low density, our formulas reduce to well-known expressions involving the scattering length of V(x).},
author = {Hainzl, Christian and Robert Seiringer},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {18},
publisher = {American Physical Society},
title = {{Critical temperature and energy gap for the BCS equation}},
doi = {10.1103/PhysRevB.77.184517},
volume = {77},
year = {2008},
}
@article{2377,
abstract = {We prove that the critical temperature for the BCS gap equation is given by T c = μ ( 8\π e γ-2+ o(1)) e π/(2μa) in the low density limit μ→ 0, with γ denoting Euler's constant. The formula holds for a suitable class of interaction potentials with negative scattering length a in the absence of bound states.},
author = {Hainzl, Christian and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {2-3},
pages = {99 -- 107},
publisher = {Springer},
title = {{The BCS critical temperature for potentials with negative scattering length}},
doi = {10.1007/s11005-008-0242-y},
volume = {84},
year = {2008},
}
@article{2378,
abstract = {We derive a lower bound on the ground state energy of the Hubbard model for given value of the total spin. In combination with the upper bound derived previously by Giuliani (J. Math. Phys. 48:023302, [2007]), our result proves that in the low density limit the leading order correction compared to the ground state energy of a non-interacting lattice Fermi gas is given by 8πaσ uσ d , where σ u(d) denotes the density of the spin-up (down) particles, and a is the scattering length of the contact interaction potential. This result extends previous work on the corresponding continuum model to the lattice case.},
author = {Robert Seiringer and Yin, Jun},
journal = {Journal of Statistical Physics},
number = {6},
pages = {1139 -- 1154},
publisher = {Springer},
title = {{Ground state energy of the low density hubbard model}},
doi = {10.1007/s10955-008-9527-x},
volume = {131},
year = {2008},
}
@article{2379,
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Journal of the American Mathematical Society},
number = {4},
pages = {925 -- 950},
publisher = {American Mathematical Society},
title = {{Hardy-Lieb-Thirring inequalities for fractional Schrödinger operators}},
doi = {10.1090/S0894-0347-07-00582-6},
volume = {21},
year = {2008},
}
@article{2380,
abstract = {The Bardeen-Cooper-Schrieffer (BCS) functional has recently received renewed attention as a description of fermionic gases interacting with local pairwise interactions. We present here a rigorous analysis of the BCS functional for general pair interaction potentials. For both zero and positive temperature, we show that the existence of a non-trivial solution of the nonlinear BCS gap equation is equivalent to the existence of a negative eigenvalue of a certain linear operator. From this we conclude the existence of a critical temperature below which the BCS pairing wave function does not vanish identically. For attractive potentials, we prove that the critical temperature is non-zero and exponentially small in the strength of the potential.},
author = {Hainzl, Christian and Hamza, Eman and Robert Seiringer and Solovej, Jan P},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {349 -- 367},
publisher = {Springer},
title = {{The BCS functional for general pair interactions}},
doi = {10.1007/s00220-008-0489-2},
volume = {281},
year = {2008},
}
@article{2381,
abstract = {We determine the sharp constant in the Hardy inequality for fractional Sobolev spaces. To do so, we develop a non-linear and non-local version of the ground state representation, which even yields a remainder term. From the sharp Hardy inequality we deduce the sharp constant in a Sobolev embedding which is optimal in the Lorentz scale. In the appendix, we characterize the cases of equality in the rearrangement inequality in fractional Sobolev spaces.},
author = {Frank, Rupert L and Robert Seiringer},
journal = {Journal of Functional Analysis},
number = {12},
pages = {3407 -- 3430},
publisher = {Academic Press},
title = {{Non-linear ground state representations and sharp Hardy inequalities}},
doi = {10.1016/j.jfa.2008.05.015},
volume = {255},
year = {2008},
}
@article{2382,
abstract = {We show that the Lieb-Liniger model for one-dimensional bosons with repulsive δ-function interaction can be rigorously derived via a scaling limit from a dilute three-dimensional Bose gas with arbitrary repulsive interaction potential of finite scattering length. For this purpose, we prove bounds on both the eigenvalues and corresponding eigenfunctions of three-dimensional bosons in strongly elongated traps and relate them to the corresponding quantities in the Lieb-Liniger model. In particular, if both the scattering length a and the radius r of the cylindrical trap go to zero, the Lieb-Liniger model with coupling constant g ∼ a/r 2 is derived. Our bounds are uniform in g in the whole parameter range 0 ≤ g ≤ ∞, and apply to the Hamiltonian for three-dimensional bosons in a spectral window of size ∼ r -2 above the ground state energy.},
author = {Robert Seiringer and Yin, Jun},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {459 -- 479},
publisher = {Springer},
title = {{The Lieb-Liniger model as a limit of dilute bosons in three dimensions}},
doi = {10.1007/s00220-008-0521-6},
volume = {284},
year = {2008},
}
@article{2383,
abstract = {We study the relativistic electron-positron field at positive temperature in the Hartree-Fock approximation. We consider both the case with and without exchange terms, and investigate the existence and properties of minimizers. Our approach is non-perturbative in the sense that the relevant electron subspace is determined in a self-consistent way. The present work is an extension of previous work by Hainzl, Lewin, Séré and Solovej where the case of zero temperature was considered.},
author = {Hainzl, Christian and Lewin, Mathieu and Robert Seiringer},
journal = {Reviews in Mathematical Physics},
number = {10},
pages = {1283 -- 1307},
publisher = {World Scientific Publishing},
title = {{A nonlinear model for relativistic electrons at positive temperature}},
doi = {10.1142/S0129055X08003547},
volume = {20},
year = {2008},
}
@inproceedings{2702,
abstract = {We review our proof that in a scaling limit, the time evolution of a quantum particle in a static random environment leads to a diffusion equation. In particular, we discuss the role of Feynman graph expansions and of renormalization.
},
author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer},
pages = {167 -- 182},
publisher = {World Scientific Publishing},
title = {{Feynman graphs and renormalization in quantum diffusion}},
doi = {10.1142/9789812833556_0011},
year = {2008},
}
@article{1763,
abstract = {The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.},
author = {Johannes Fink and Göppl, M and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas},
journal = {Nature},
number = {7202},
pages = {315 -- 318},
publisher = {Nature Publishing Group},
title = {{Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system}},
doi = {10.1038/nature07112},
volume = {454},
year = {2008},
}
@article{1765,
abstract = {High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.},
author = {Göppl, M and Fragner, A and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Johannes Fink and Leek, Peter J and Puebla, G and Steffen, L. Kraig and Wallraff, Andreas},
journal = {Journal of Applied Physics},
number = {11},
publisher = {American Institute of Physics},
title = {{Coplanar waveguide resonators for circuit quantum electrodynamics}},
doi = {10.1063/1.3010859},
volume = {104},
year = {2008},
}
@article{2120,
abstract = {We consider the linear stochastic Cauchy problem dX (t) =AX (t) dt +B dWH (t), t≥ 0, where A generates a C0-semigroup on a Banach space E, WH is a cylindrical Brownian motion over a Hilbert space H, and B: H → E is a bounded operator. Assuming the existence of a unique minimal invariant measure μ∞, let Lp denote the realization of the Ornstein-Uhlenbeck operator associated with this problem in Lp (E, μ∞). Under suitable assumptions concerning the invariance of the range of B under the semigroup generated by A, we prove the following domain inclusions, valid for 1 < p ≤ 2: Image omitted. Here WHk, p (E, μinfin; denotes the kth order Sobolev space of functions with Fréchet derivatives up to order k in the direction of H. No symmetry assumptions are made on L p.},
author = {Jan Maas and van Neerven, Jan M},
journal = {Infinite Dimensional Analysis, Quantum Probability and Related Topics},
number = {4},
pages = {603 -- 626},
publisher = {World Scientific Publishing},
title = {{On the domain of non-symmetric Ornstein-Uhlenbeck operators in banach spaces}},
doi = {10.1142/S0219025708003245},
volume = {11},
year = {2008},
}
@article{2121,
abstract = {Let H be a separable real Hubert space and let double struck F sign = (ℱt)t∈[0,T] be the augmented filtration generated by an H-cylindrical Brownian motion (WH(t))t∈[0,T] on a probability space (Ω, ℱ ℙ). We prove that if E is a UMD Banach space, 1 ≤ p < ∞, and F ∈ double struck D sign1,p(Ω E) is ℱT-measurable, then F = double struck E sign(F) + ∫0T Pdouble struck F sign(DF) dW H, where D is the Malliavin derivative of F and P double struck F sign is the projection onto the F-adapted elements in a suitable Banach space of Lp-stochastically integrable ℒ(H, E)-valued processes.},
author = {van Neerven, Jan M and Jan Maas},
journal = {Electronic Communications in Probability},
pages = {151 -- 164},
publisher = {Institute of Mathematical Statistics},
title = {{A Clark-Ocone formula in UMD Banach spaces}},
volume = {13},
year = {2008},
}
@article{2146,
abstract = {We present an analytic model of thermal state-to-state rotationally inelastic collisions of polar molecules in electric fields. The model is based on the Fraunhofer scattering of matter waves and requires Legendre moments characterizing the “shape” of the target in the body-fixed frame as its input. The electric field orients the target in the space-fixed frame and thereby effects a striking alteration of the dynamical observables: both the phase and amplitude of the oscillations in the partial differential cross sections undergo characteristic field-dependent changes that transgress into the partial integral cross sections. As the cross sections can be evaluated for a field applied parallel or perpendicular to the relative velocity, the model also offers predictions about steric asymmetry. We exemplify the field-dependent quantum collision dynamics with the behavior of the Ne–OCS(Σ1) and Ar–NO(Π2) systems. A comparison with the close-coupling calculations available for the latter system [Chem. Phys. Lett.313, 491 (1999)] demonstrates the model’s ability to qualitatively explain the field dependence of all the scattering features observed.},
author = {Mikhail Lemeshko and Friedrich, Břetislav},
journal = {Journal of Chemical Physics},
number = {2},
publisher = {American Institute of Physics},
title = {{An analytic model of rotationally inelastic collisions of polar molecules in electric fields}},
doi = {10.1063/1.2948392},
volume = {129},
year = {2008},
}
@article{6146,
abstract = {Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies.},
author = {Bretscher, A. J. and Busch, K. E. and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {23},
pages = {8044--8049},
publisher = {Proceedings of the National Academy of Sciences},
title = {{A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans}},
doi = {10.1073/pnas.0707607105},
volume = {105},
year = {2008},
}
@article{1460,
abstract = {We calculate the E-polynomials of certain twisted GL(n,ℂ)-character varieties Mn of Riemann surfaces by counting points over finite fields using the character table of the finite group of Lie-type GL(n, q) and a theorem proved in the appendix by N. Katz. We deduce from this calculation several geometric results, for example, the value of the topological Euler characteristic of the associated PGL(n,ℂ)-character variety. The calculation also leads to several conjectures about the cohomology of Mn: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable representations of a certain quiver. We prove these conjectures for n=2.},
author = {Tamas Hausel and Rodríguez Villegas, Fernando},
journal = {Inventiones Mathematicae},
number = {3},
pages = {555 -- 624},
publisher = {Springer},
title = {{Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz}},
doi = {10.1007/s00222-008-0142-x},
volume = {174},
year = {2008},
}
@article{1036,
abstract = {We report on the control of interaction-induced dephasing of Bloch oscillations for an atomic Bose-Einstein condensate in an optical lattice. We quantify the dephasing in terms of the width of the quasimomentum distribution and measure its dependence on time for different interaction strengths which we control by means of a Feshbach resonance. For minimal interaction, the dephasing time is increased from a few to more than 20 thousand Bloch oscillation periods, allowing us to realize a BEC-based atom interferometer in the noninteracting limit.},
author = {Gustavsson, Mattias and Haller, Elmar and Mark, Manfred and Danzl, Johann G and Rojas Kopeinig, Gabriel and Nägerl, Hanns},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Control of interaction-induced dephasing of bloch oscillations}},
doi = {10.1103/PhysRevLett.100.080404},
volume = {100},
year = {2008},
}
@article{1037,
abstract = {We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation threshold, which are stable against spontaneous decay on the time scale of 1s. An optically trapped sample of ultracold dimers is prepared in a high rotational state and magnetically tuned into a region with a negative binding energy. The metastable character of these molecules arises from the large centrifugal barrier in combination with negligible coupling to states with low rotational angular momentum. A sharp onset of dissociation with increasing magnetic field is mediated by a crossing with a lower rotational dimer state and facilitates dissociation on demand with a well-defined energy.},
author = {Knoop, Steven and Mark, Michael and Ferlaino, Francesca and Danzl, Johann G and Kraemer, Tobias and Nägerl, Hanns and Grimm, Rudolf},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Metastable feshbach molecules in high rotational states}},
doi = {10.1103/PhysRevLett.100.083002},
volume = {100},
year = {2008},
}
@article{1039,
abstract = {Molecular cooling techniques face the hurdle of dissipating translational as well as internal energy in the presence of a rich electronic, vibrational, and rotational energy spectrum. In our experiment, we create a translationally ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers in the electronic ground state. Specifically, we stimulate with 80% efficiency, a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein condensate of cesium atoms. In the process, the initial loose, long-range electrostatic bond of the Feshbach molecule is coherently transformed into a tight chemical bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and show that the molecular sample is not heated during the transfer. Our results show that the preparation of a quantum gas of molecules in specific rovibrational states is possible and that the creation of a Bose-Einstein condensate of molecules in their rovibronic ground state is within reach.},
author = {Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Hart, Russell and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Nägerl, Hanns},
journal = {Science},
number = {5892},
pages = {1062 -- 1066},
publisher = {American Association for the Advancement of Science},
title = {{Quantum gas of deeply bound ground state molecules}},
doi = {10.1126/science.1159909},
volume = {321},
year = {2008},
}
@article{965,
abstract = {We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.},
author = {Morozov, Alexei Y and Maksym Serbyn},
journal = {Theoretical and Mathematical Physics},
number = {2},
pages = {270 -- 293},
publisher = {Elsevier},
title = {{Nonlinear algebra and Bogoliubov's recursion}},
doi = {10.1007/s11232-008-0026-7},
volume = {154},
year = {2008},
}
@article{3734,
abstract = {Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally.},
author = {Gasper Tkacik and Gregor, Thomas and Bialek, William S},
journal = {PLoS One},
number = {7},
publisher = {Public Library of Science},
title = {{The role of input noise in transcriptional regulation}},
doi = {10.1371/journal.pone.0002774},
volume = {3},
year = {2008},
}
@article{3740,
abstract = {In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission.},
author = {Gasper Tkacik and Callan,Curtis G and Bialek, William S},
journal = {PNAS},
number = {34},
pages = {12265 -- 12270},
publisher = {National Academy of Sciences},
title = {{Information flow and optimization in transcriptional regulation}},
doi = {10.1073/pnas.0806077105},
volume = {105},
year = {2008},
}
@article{3744,
abstract = {It is widely acknowledged that detailed timing of action potentials is used to encode information, for example, in auditory pathways; however, the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much that they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel.},
author = {Gasper Tkacik and Magnasco, Marcelo O},
journal = {Biosystems},
number = {1-2},
pages = {90 -- 100},
publisher = {Elsevier},
title = {{Decoding spike timing: The differential reverse-correlation method}},
doi = {10.1016/j.biosystems.2008.04.011},
volume = {93},
year = {2008},
}
@article{3751,
abstract = {Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator sequences binding activators and repressors-of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling.},
author = {Kinkhabwala, Ali and Guet, Calin C},
journal = {PLoS One},
number = {4},
publisher = {Public Library of Science},
title = {{Uncovering cis regulatory codes using synthetic promoter shuffling}},
doi = {10.1371/journal.pone.0002030},
volume = {3},
year = {2008},
}
@article{3822,
abstract = {Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole-cell recordings from granule cells in acute hippocampal slices of adult mice at approximately 23 degrees C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 +/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at approximately 20-30 mum distance from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1). Qualitatively similar results were obtained at a recording temperature of approximately 34 degrees C. Modelling of AP propagation in detailed cable models of granule cells suggested that a approximately 4 times higher Na(+) channel density ( approximately 1000 pS mum(-2)) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output.},
author = {Schmidt-Hieber, Christoph and Peter Jonas and Bischofberger, Josef},
journal = {Journal of Physiology},
number = {7},
pages = {1849 -- 57},
publisher = {Wiley-Blackwell},
title = {{Action potential initiation and propagation in hippocampal mossy fibre axons}},
doi = {10.1113/jphysiol.2007.150151 },
volume = {586},
year = {2008},
}
@article{3825,
abstract = {Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type of inhibitory interneuron in the hippocampus. These cells inhibit principal cells in a temporally precise manner and are involved in the generation of network oscillations. Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling in these interneurons has not been investigated. To study action potential (AP)-induced dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2 or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that increased linearly with AP number. Analysis of Ca(2+) transients under steady-state conditions with different fura-2 concentrations and during loading with 200 microm fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200 (kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1). At approximately 23 degrees C, the decay time constant of the Ca(2+) transients was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At 34 degrees C, the decay time constant was 203 ms and the corresponding extrusion rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst activity with three to five APs per theta cycle, as occurs in vivo during exploration, led to a moderate increase in the global Ca(2+) concentration that was proportional to AP number, whereas more intense stimulation was required to reach micromolar Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime. In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio, a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion. These specific buffering properties of BCs will sharpen the time course of local Ca(2+) signals, while prolonging the decay of global Ca(2+) signals.},
author = {Aponte, Yexica and Bischofberger, Josef and Peter Jonas},
journal = {Journal of Physiology},
number = {8},
pages = {2061 -- 75},
publisher = {Wiley-Blackwell},
title = {{Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus}},
doi = {10.1113/jphysiol.2007.147298},
volume = {586},
year = {2008},
}
@inproceedings{3878,
abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing “reset” action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Majumdar, Ritankar S},
pages = {91 -- 106},
publisher = {Springer},
title = {{The complexity of coverage}},
doi = {10.1007/978-3-540-89330-1_7},
volume = {5356},
year = {2008},
}
@inproceedings{4384,
abstract = {Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.
Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system.},
author = {Guerraoui, Rachid and Thomas Henzinger and Jobstmann, Barbara and Vasu Singh},
pages = {372 -- 382},
publisher = {ACM},
title = {{Model checking transactional memories}},
doi = {10.1145/1375581.1375626},
year = {2008},
}
@article{3037,
author = {Feraru, Elena and Friml, Jirí},
journal = {Plant Physiology},
number = {4},
pages = {1553 -- 1559},
publisher = {American Society of Plant Biologists},
title = {{PIN polar targeting}},
doi = {10.1104/pp.108.121756},
volume = {147},
year = {2008},
}
@article{3307,
abstract = {A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.},
author = {Green, Richard E and Malaspinas, Anna-Sapfo and Krause, Johannes and Briggs, Adrian W and Johnson, Philip L and Caroline Uhler and Meyer, Matthias and Good, Jeffrey M and Maricic, Tomislav and Stenzel, Udo and Prüfer, Kay and Siebauer, Michael F and Burbano, Hernän A and Ronan, Michael T and Rothberg, Jonathan M and Egholm, Michael and Rudan, Pavao and Brajković, Dejana and Kućan, Željko and Gušić, Ivan and Wikström, Mårten K and Laakkonen, Liisa J and Kelso, Janet F and Slatkin, Montgomery and Pääbo, Svante H},
journal = {Cell},
pages = {416 -- 426},
publisher = {Cell Press},
title = {{A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing}},
doi = {10.1016/j.cell.2008.06.021},
volume = {134},
year = {2008},
}