@article{1752, abstract = {The epitaxial growth of germanium on silicon leads to the self-assembly of SiGe nanocrystals by a process that allows the size, composition and position of the nanocrystals to be controlled. This level of control, combined with an inherent compatibility with silicon technology, could prove useful in nanoelectronic applications. Here, we report the confinement of holes in quantum-dot devices made by directly contacting individual SiGe nanocrystals with aluminium electrodes, and the production of hybrid superconductor- semiconductor devices, such as resonant supercurrent transistors, when the quantum dot is strongly coupled to the electrodes. Charge transport measurements on weakly coupled quantum dots reveal discrete energy spectra, with the confined hole states displaying anisotropic gyromagnetic factors and strong spin-orbit coupling with pronounced dependences on gate voltage and magnetic field.}, author = {Georgios Katsaros and Spathis, Panayotis N and Stoffel, Mathieu and Fournel, Frank and Mongillo, Massimo and Bouchiat, Vincent and Lefloch, François and Rastelli, Armando and Schmidt, Oliver G and De Franceschi, Silvano}, journal = {Nature Nanotechnology}, number = {6}, pages = {458 -- 464}, publisher = {Nature Publishing Group}, title = {{Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals on silicon}}, doi = {10.1038/nnano.2010.84}, volume = {5}, year = {2010}, } @article{1753, abstract = {We investigate electronic transport in n-i-n GaN nanowires with and without AlN double barriers. The nanowires are grown by catalyst-free, plasma-assisted molecular beam epitaxy enabling abrupt GaN/AlN interfaces as well as longitudinal n-type doping modulation. At low temperature, transport in n-i-n GaN nanowires is dominated by the Coulomb blockade effect. Carriers are confined in the undoped middle region, forming single or multiple islands with a characteristic length of ∼100 nm. The incorporation of two AlN tunnel barriers causes confinement to occur within the GaN dot in between. In the case of a 6 nm thick dot and 2 nm thick barriers, we observe characteristic signatures of Coulomb-blockaded transport in single quantum dots with discrete energy states. For thinner dots and barriers, Coulomb-blockade effects do not play a significant role while the onset of resonant tunneling via the confined quantum levels is accompanied by a negative differential resistance surviving up to ∼150 K.}, author = {Songmuang, Rudeeson and Georgios Katsaros and Monroy, Eva and Spathis, Panayotis N and Bougerol, Catherine and Mongillo, Massimo and De Franceschi, Silvano}, journal = {Nano Letters}, number = {9}, pages = {3545 -- 3550}, publisher = {American Chemical Society}, title = {{Quantum transport in GaN/AlN double-barrier heterostructure nanowires}}, doi = {10.1021/nl1017578}, volume = {10}, year = {2010}, } @article{1773, abstract = {The quantum properties of electromagnetic, mechanical or other harmonic oscillators can be revealed by investigating their strong coherent coupling to a single quantum two level system in an approach known as cavity quantum electrodynamics (QED). At temperatures much lower than the characteristic energy level spacing the observation of vacuum Rabi oscillations or mode splittings with one or a few quanta asserts the quantum nature of the oscillator. Here, we study how the classical response of a cavity QED system emerges from the quantum one when its thermal occupation-or effective temperature-is raised gradually over 5 orders of magnitude. In this way we explore in detail the continuous quantum-to-classical crossover and demonstrate how to extract effective cavity field temperatures from both spectroscopic and time-resolved vacuum Rabi measurements.}, author = {Johannes Fink and Steffen, L. Kraig and Studer, Peter and Bishop, Lev S and Baur, Matthias P and Bianchetti, R and Bozyigit, Deniz and Lang, C and Filipp, Stefan and Leek, Peter J and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Quantum-to-classical transition in cavity quantum electrodynamics}}, doi = {10.1103/PhysRevLett.105.163601}, volume = {105}, year = {2010}, } @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{13409, abstract = {The immobilization of molecular switches onto inorganic supports has recently become a hot topic as it can give rise to novel hybrid materials in which the properties of the two components are mutually enhanced. Even more attractive is the concept of “transferring” the switchable characteristics of single layers of organic molecules onto the underlying inorganic components, rendering them responsive to external stimuli as well. Of the various molecular switches studied, azobenzene (AB) has arguably attracted most attention due to its simple molecular structure, and because its “trigger” (light) is a noninvasive one, it can be delivered instantaneously, and into a precise location. In order to fully realize its potential, however, it is necessary to immobilize AB onto solid supports. It is the goal of this manuscript to comprehensively yet concisely review such hybrid systems which comprise AB forming well-defined self-assembled monolayers (SAMs) on planar and curved (colloidal and nanoporous) inorganic surfaces. I discuss methods to immobilize AB derivatives onto surfaces, strategies to ensure efficient AB isomerization, ways to monitor the switching process, properties of these switchable hybrid materials, and, last but not least, their emerging applications.}, author = {Klajn, Rafal}, issn = {1365-3075}, journal = {Pure and Applied Chemistry}, keywords = {General Chemical Engineering, General Chemistry}, number = {12}, pages = {2247--2279}, publisher = {De Gruyter}, title = {{Immobilized azobenzenes for the construction of photoresponsive materials}}, doi = {10.1351/pac-con-10-09-04}, 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}, } @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{10127, abstract = {We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-683X}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {5}, pages = {1874--1878}, publisher = {Royal Society of Chemistry (RSC)}, title = {{Particle self-assembly on soft elastic shells}}, doi = {10.1039/c0sm01143f}, volume = {7}, year = {2010}, } @article{10390, abstract = {We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases, which includes most of the mesophases observed in self-assembly of block copolymers but also crystalline structures formed by asymmetric, hard binary mixtures. Our results detail the phenomenological behavior of these systems when softness is introduced in terms of two different classes of interparticle interactions: (a) the elastic Hertz potential, which has a finite energy cost for complete overlap of any two components, and (b) a generic power-law repulsion with tunable exponent. We discuss how simple geometric arguments can be used to account for the large structural variety observed in these systems and detail the similarities and differences in the phase behavior for the two classes of potentials under consideration.}, author = {Šarić, Anđela and Bozorgui, Behnaz and Cacciuto, Angelo}, issn = {1520-5207}, journal = {The Journal of Physical Chemistry B}, keywords = {materials chemistry}, number = {22}, pages = {7182--7189}, publisher = {American Chemical Society}, title = {{Packing of soft asymmetric dumbbells}}, doi = {10.1021/jp107545w}, volume = {115}, year = {2010}, } @article{10391, abstract = {We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results.}, author = {Šarić, Anđela and Pàmies, Josep C. and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {22}, publisher = {American Physical Society}, title = {{Effective elasticity of a flexible filament bound to a deformable cylindrical surface}}, doi = {10.1103/physrevlett.104.226101}, volume = {104}, 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}, }