@inbook{164,
  abstract     = {Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method.},
  author       = {Browning, Timothy D and Heath Brown, Roger},
  booktitle    = {Analytic Number Theory: Essays in honour of Klaus Roth},
  pages        = {75 -- 90},
  publisher    = {Cambridge University Press},
  title        = {{Integral points on cubic hypersurfaces}},
  year         = {2009},
}

@article{1766,
  abstract     = {We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation.},
  author       = {Leek, Peter J and Filipp, Stefan and Maurer, Patrick and Baur, Matthias P and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Wallraff, Andreas},
  journal      = {Physical Review B - Condensed Matter and Materials Physics},
  number       = {18},
  publisher    = {American Physical Society},
  title        = {{Using sideband transitions for two-qubit operations in superconducting circuits}},
  doi          = {10.1103/PhysRevB.79.180511},
  volume       = {79},
  year         = {2009},
}

@article{1767,
  abstract     = {We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives.},
  author       = {Baur, Matthias P and Filipp, Stefan and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Physical Review Letters},
  number       = {24},
  publisher    = {American Physical Society},
  title        = {{Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit}},
  doi          = {10.1103/PhysRevLett.102.243602},
  volume       = {102},
  year         = {2009},
}

@article{1768,
  abstract     = {Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states.},
  author       = {Filipp, Stefan and Maurer, Patrick and Leek, Peter J and Baur, Matthias P and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Gambetta, Jay M and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Physical Review Letters},
  number       = {20},
  publisher    = {American Physical Society},
  title        = {{Two-qubit state tomography using a joint dispersive readout}},
  doi          = {10.1103/PhysRevLett.102.200402},
  volume       = {102},
  year         = {2009},
}

@article{1769,
  abstract     = {We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers.},
  author       = {Johannes Fink and Bianchetti, R and Baur, Matthias P and Göppl, M and Steffen, L. Kraig and Filipp, Stefan and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Physical Review Letters},
  number       = {8},
  publisher    = {American Physical Society},
  title        = {{Dressed collective qubit states and the Tavis-Cummings model in circuit QED}},
  doi          = {10.1103/PhysRevLett.103.083601},
  volume       = {103},
  year         = {2009},
}

@article{1770,
  abstract     = {The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.},
  author       = {Bianchetti, R and Filipp, Stefan and Baur, Matthias P and Johannes Fink and Göppl, M and Leek, Peter J and Steffen, L. Kraig and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Physical Review A - Atomic, Molecular, and Optical Physics},
  number       = {4},
  publisher    = {American Physical Society},
  title        = {{Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics}},
  doi          = {10.1103/PhysRevA.80.043840},
  volume       = {80},
  year         = {2009},
}

@article{1771,
  abstract     = {The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits.},
  author       = {Johannes Fink and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Göppl, M and Leek, Peter J and Steffen, L. Kraig and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Physica Scripta T},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics}},
  doi          = {10.1088/0031-8949/2009/T137/014013},
  volume       = {T137},
  year         = {2009},
}

@article{1825,
  abstract     = {Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model. },
  author       = {Tamar Friedlander and Brenner, Naama},
  journal      = {PNAS},
  number       = {52},
  pages        = {22558 -- 22563},
  publisher    = {National Academy of Sciences},
  title        = {{Adaptive response by state-dependent inactivation}},
  doi          = {10.1073/pnas.0902146106 },
  volume       = {106},
  year         = {2009},
}

@misc{5392,
  abstract     = {We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs of [GO09] and present a precise characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems.},
  author       = {Chatterjee, Krishnendu},
  issn         = {2664-1690},
  pages        = {17},
  publisher    = {IST Austria},
  title        = {{Probabilistic automata on infinite words: Decidability and undecidability results}},
  doi          = {10.15479/AT:IST-2009-0004},
  year         = {2009},
}

@misc{5393,
  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 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},
  issn         = {2664-1690},
  pages        = {12},
  publisher    = {IST Austria},
  title        = {{Gist: A solver for probabilistic games}},
  doi          = {10.15479/AT:IST-2009-0003},
  year         = {2009},
}

@misc{5394,
  abstract     = {We consider two-player games played on graphs with request-response and finitary Streett objectives. We show these games are PSPACE-hard, improving the previous known NP-hardness. We also improve the lower bounds on memory required by the winning strategies for the players.},
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian},
  issn         = {2664-1690},
  pages        = {11},
  publisher    = {IST Austria},
  title        = {{Improved lower bounds for request-response and finitary Streett games}},
  doi          = {10.15479/AT:IST-2009-0002},
  year         = {2009},
}

@misc{5395,
  abstract     = {We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with omega-regular objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observa- tions. We consider the qualitative analysis problem: given a POMDP with an omega-regular objective, whether there is 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 of POMDPs with parity objectives (a canonical form to express omega-regular objectives) and its subclasses. Our contribution consists in establishing several upper and lower bounds that were not known in literature. Second, we present optimal bounds (matching upper and lower bounds) on the memory required by pure and randomized observation-based strategies for the qualitative analysis of POMDPs with parity objectives and its subclasses.},
  author       = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
  issn         = {2664-1690},
  pages        = {20},
  publisher    = {IST Austria},
  title        = {{Qualitative analysis of partially-observable Markov decision processes}},
  doi          = {10.15479/AT:IST-2009-0001},
  year         = {2009},
}

@article{599,
  abstract     = {The human CDK8 subcomplex (CDK8, cyclin C, Med12, and Med13) negatively regulates transcription in ways not completely defined; past studies suggested CDK8 kinase activity was required for its repressive function. Using a reconstituted transcription system together with recombinant or endogenous CDK8 subcomplexes, we demonstrate that, in fact, Med12 and Med13 are critical for subcomplex-dependent repression, whereas CDK8 kinase activity is not. A hallmark of activated transcription is efficient reinitiation from promoter-bound scaffold complexes that recruit a series of pol II enzymes to the gene. Notably, the CDK8 submodule strongly represses even reinitiation events, suggesting a means to fine tune transcript levels. Structural and biochemical studies confirm the CDK8 submodule binds the Mediator leg/tail domain via the Med13 subunit, and this submodule-Mediator association precludes pol II recruitment. Collectively, these results reveal the CDK8 subcomplex functions as a simple switch that controls the Mediator-pol II interaction to help regulate transcription initiation and reinitiation events. As Mediator is generally required for expression of protein-coding genes, this may reflect a common mechanism by which activated transcription is shut down in human cells.},
  author       = {Knuesel, Matthew and Meyer, Krista and Bernecky, Carrie A and Taatjes, Dylan},
  journal      = {Genes and Development},
  number       = {4},
  pages        = {439 -- 451},
  publisher    = {Cold Spring Harbor Laboratory Press},
  title        = {{The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function}},
  doi          = {10.1101/gad.1767009},
  volume       = {23},
  year         = {2009},
}

@article{1038,
  abstract     = {One possible way to produce ultra-cold, high-phase-space-density quantum gases of molecules in the rovibronic ground state is given by molecule association from quantum-degenerate atomic gases on a Feshbach resonance and subsequent coherent optical multi-photon transfer into the rovibronic ground state. In ultra-cold samples of Cs2 molecules, we observe two-photon dark resonances that connect the intermediate rovibrational level |v=73,J=2 with the rovibrational ground state |v=0,J=0 of the singlet X 1 ∑ g + ground-state potential. For precise dark resonance spectroscopy we exploit the fact that it is possible to efficiently populate the level |v=73,J=2 by two-photon transfer from the dissociation threshold with the stimulated Raman adiabatic passage (STIRAP) technique. We find that at least one of the two-photon resonances is sufficiently strong to allow future implementation of coherent STIRAP transfer of a molecular quantum gas to the rovibrational ground state |v=0,J=0.},
  author       = {Mark, Manfred and Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Bouloufa, Nadia and Dulieu, Olivier and Salami, Houssam and Bergeman, Thomas and Ritsch, Helmut and Hart, Russell and Nägerl, Hanns},
  journal      = {Applied Physics B: Lasers and Optics},
  number       = {2},
  pages        = {219 -- 225},
  publisher    = {Springer},
  title        = {{Dark resonances for ground-state transfer of molecular quantum gases}},
  doi          = {10.1007/s00340-009-3407-1},
  volume       = {95},
  year         = {2009},
}

@article{1040,
  abstract     = {Ultracold atomic physics offers myriad possibilities to study strongly correlated many-body systems in lower dimensions. Typically, only ground-state phases are accessible. Using a tunable quantum gas of bosonic cesium atoms, we realized and controlled in one-dimensional geometry a highly excited quantum phase that is stabilized in the presence of attractive interactions by maintaining and strengthening quantum correlations across a confinement-induced resonance. We diagnosed the crossover from repulsive to attractive interactions in terms of the stiffness and energy of the system. Our results open up the experimental study of metastable, excited, many-body phases with strong correlations and their dynamical properties.},
  author       = {Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Danzl, Johann G and Hart, Russell and Pupillo, Guido and Nägerl, Hanns},
  journal      = {Science},
  number       = {5945},
  pages        = {1224 -- 1227},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Realization of an excited, strongly correlated quantum gas Phase}},
  doi          = {10.1126/science.1175850},
  volume       = {325},
  year         = {2009},
}

@article{1041,
  abstract     = {We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that the lifetime in the lattice is limited by optical excitation by the lattice light. The molecule trapping time for a lattice depth of 15 atomic recoil energies is about 20 ms. We determine the trapping frequency by the lattice phase and amplitude modulation technique. It will now be possible to transfer the molecules to the rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice.},
  author       = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Hart, Russell and Liem, Andreas and Zellmer, Holger and Nägerl, Hanns},
  journal      = {New Journal of Physics},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Deeply bound ultracold molecules in an optical lattice}},
  doi          = {10.1088/1367-2630/11/5/055036},
  volume       = {11},
  year         = {2009},
}

@article{1043,
  abstract     = {One possibility for the creation of ultracold, high phase space density quantum gases of molecules in the rovibronic ground state relies on first associating weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance and then transferring the molecules via several steps of coherent two-photon stimulated Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms, we observe several optical transitions to deeply-bound rovibrational levels of the excited 0 u+ molecular potentials with high resolution. At least one of these transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound vibrational level v = 73> of the singlet X 1Σg+ ground state potential, as recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062). From this level, the rovibrational ground state v = 0, J = 0> can be reached with one more transfer step. In total, our results show that coherent ground state transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP processes or one single four-photon STIRAP process.},
  author       = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Hart, Russell and Nägerl, Hanns},
  journal      = {Faraday Discussions},
  pages        = {283 -- 295},
  publisher    = {Royal Society of Chemistry},
  title        = {{Precision molecular spectroscopy for ground state transfer of molecular quantum gases}},
  doi          = {10.1039/b820542f},
  volume       = {142},
  year         = {2009},
}

@article{9453,
  abstract     = {Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.},
  author       = {Hsieh, Tzung-Fu and Ibarra, Christian A. and Silva, Pedro and Zemach, Assaf and Eshed-Williams, Leor and Fischer, Robert L. and Zilberman, Daniel},
  issn         = {1095-9203},
  journal      = {Science},
  keywords     = {Multidisciplinary},
  number       = {5933},
  pages        = {1451--1454},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Genome-wide demethylation of Arabidopsis endosperm}},
  doi          = {10.1126/science.1172417},
  volume       = {324},
  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},
}

@unpublished{3732,
  abstract     = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the salamander retina responding to natural movies. We show that pairwise interactions between neurons account for observed higher-order correlations, and that for groups of 10 or more neurons pairwise interactions can no longer be regarded as small perturbations in an independent system. We then construct network ensembles that generalize the network instances observed in the experiment, and study their thermodynamic behavior and coding capacity. Based on this construction, we can also create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. We examine closely two such behaviors that could be relevant for neural code: tuning of the network to the critical point to maximize the ability to encode diverse stimuli, and using the metastable states of the Ising Hamiltonian as neural code words.},
  author       = {Gasper Tkacik and Schneidman, Elad and Berry, Michael J and Bialek, William S},
  booktitle    = {ArXiv},
  publisher    = {ArXiv},
  title        = {{Spin glass models for a network of real neurons}},
  volume       = {q-bio.NC},
  year         = {2009},
}