@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{13410, abstract = {A range (Au, Pt, Pd) of metal nanoparticles (MNPs) has been prepared and functionalized with (a) redox-active stalks containing tetrathiafulvalene (TTF) units, (b) [2]pseudorotaxanes formed between these stalks and cyclobis(paraquat-p-phenylene) (CBPQT4+) rings, and (c) bistable [2]rotaxane molecules where the dumbbell component contains a 1,5-dioxynaphthalene (DNP) unit, as well as a TTF unit, encircled by a CBPQT4+ ring. It transpires that the molecules present in (a) and (c) and the supermolecules described in (b) retain their switching characteristics, previously observed in solution, when they are immobilized onto MNPs. Moreover, their oxidation potentials depend on the fraction, χ, of the molecules or supermolecules on the surface of the nanoparticles. A variation in χ affects the oxidation potentials of the TTF units to the extent that switching can be subjected to fine tuning as a result. Specifically, increasing χ results in positive shifts (i) in the oxidation potentials of the TTF unit in (a)−(c) and (ii) the reduction potentials of the CBPQT4+ rings in (c). These shifts can be attributed to an increase in the electrostatic potential surrounding the MNPs. Both the magnitude and the direction of these shifts are reproduced by a model, based on the Poisson−Boltzmann equation coupled with charge-regulating boundary conditions. Furthermore, the kinetics of relaxation from the metastable state coconformation (MSCC) to the ground-state coconformation (GSCC) of the bistable [2]rotaxane molecules also depends on χ, as well as on the nanoparticle diameter. Increasing either of these parameters accelerates the rate of relaxation from the MSCC to the GSCC. This rate is a function of (i) the activation energy for the relaxation process associated with the bistable [2]rotaxane molecules in solution and (ii) the electrostatic potential surrounding the MNPs. The electrostatic potential depends on (i) the diameter of the MNPs, (ii) the amount of the bistable [2]rotaxane molecules on the surface of the MNPs, and (iii) the equilibrium distribution of the CBPQT4+ rings between the DNP and TTF recognition sites in the GSCC. This electrostatic potential has also been quantified using the Poisson−Boltzmann equation, leading to faithful estimates of the rate constants.}, author = {Coskun, Ali and Wesson, Paul J. and Klajn, Rafal and Trabolsi, Ali and Fang, Lei and Olson, Mark A. and Dey, Sanjeev K. and Grzybowski, Bartosz A. and Stoddart, J. Fraser}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {12}, pages = {4310--4320}, publisher = {American Chemical Society}, title = {{Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory}}, doi = {10.1021/ja9102327}, volume = {132}, year = {2010}, } @article{13411, abstract = {Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide a basis for sensors that “remember” whether the sample has ever exceeded the melting temperature of the matrix. The operation of these sensors rests on the ability to photoinduce metastable electric dipoles on NP surfaces – upon melting, these dipoles drive NP aggregation, precipitation, and crosslinking. These events are manifested by a pronounced color change.}, author = {Klajn, Rafal and Browne, Kevin P. and Soh, Siowling and Grzybowski, Bartosz A.}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {13}, pages = {1385--1387}, publisher = {Wiley}, title = {{Nanoparticles that “remember” temperature}}, doi = {10.1002/smll.200902272}, volume = {6}, year = {2010}, } @article{13412, abstract = {Nanoparticles (NPs) and molecular/supramolecular switches have attracted considerable interest during the past decade on account of their unique properties and prominent roles in the fields of organic chemistry and materials science. Materials derived from the combination of these two components are now emerging in the literature. This critical review evaluates materials which comprise NPs functionalised with well-defined self-assembled monolayers of molecular and supramolecular switches. We draw attention to the fact that immobilisation of switches on NPs does not, in general, hamper their switching ability, although it can impart new properties on the supporting particles. This premise leads us to the discussion of systems in which switching on the surfaces of NPs can be used to modulate reversibly a range of NP properties—optical, fluorescent, electrical, magnetic—as well as the controlled release of small molecules. Finally, we discuss examples in which molecular switches direct reversible self-assembly of NPs (308 references).}, author = {Klajn, Rafal and Stoddart, J. Fraser and Grzybowski, Bartosz A.}, issn = {1460-4744}, journal = {Chemical Society Reviews}, keywords = {General Chemistry}, number = {6}, pages = {2203--2237}, publisher = {Royal Society of Chemistry}, title = {{Nanoparticles functionalised with reversible molecular and supramolecular switches}}, doi = {10.1039/b920377j}, volume = {39}, 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}, } @inbook{14983, abstract = {This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data.}, author = {Schlögl, Alois and Vidaurre, Carmen and Müller, Klaus-Robert}, booktitle = {Brain-Computer Interfaces}, editor = {Graimann, Bernhard and Pfurtscheller, Gert and Allison, Brendan}, isbn = {9783642020902}, issn = {1612-3018}, pages = {331--355}, publisher = {Springer}, title = {{Adaptive Methods in BCI Research - An Introductory Tutorial}}, doi = {10.1007/978-3-642-02091-9_18}, year = {2010}, } @article{1970, abstract = {Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the α-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 Å resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-Å long amphipathic α-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 Å resolution. The L-shaped assembly consists of the α-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic α-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.}, author = {Efremov, Rouslan G and Baradaran, Rozbeh and Leonid Sazanov}, journal = {Nature}, number = {7297}, pages = {441 -- 445}, publisher = {Nature Publishing Group}, title = {{The architecture of respiratory complex I}}, doi = {10.1038/nature09066}, volume = {465}, year = {2010}, } @book{4346, abstract = {With the term "Library 2.0" the editors mean an institution which applies the principles of the Web 2.0 such as openness, re-use, collaboration and interaction in the entire organization. Libraries are extending their service offerings and work processes to include the potential of Web 2.0 technologies. This changes the job description and self-image of librarians. The collective volume offers a complete overview of the topic Library 2.0 and the current state of developments from a technological, sociological, information theoretical and practice-oriented perspective.}, editor = {Danowski, Patrick and Bergmann, Julia}, isbn = {9-783-1102-3209-7}, pages = {405}, publisher = {De Gruyter}, title = {{Handbuch Bibliothek 2.0}}, doi = {10.1515/9783110232103}, volume = { 41}, year = {2010}, } @article{4358, abstract = {Phenotypic biotyping has traditionally been used to differentiate bacteria occupying distinct ecological niches such as host species. For example, the capacity of Staphylococcus aureus from sheep to coagulate ruminant plasma, reported over 60 years ago, led to the description of small ruminant and bovine S. aureus ecovars. The great majority of small ruminant isolates are represented by a single, widespread clonal complex (CC133) of S. aureus, but its evolutionary origin and the molecular basis for its host tropism remain unknown. Here, we provide evidence that the CC133 clone evolved as the result of a human to ruminant host jump followed by adaptive genome diversification. Comparative whole-genome sequencing revealed molecular evidence for host adaptation including gene decay and diversification of proteins involved in host-pathogen interactions. Importantly, several novel mobile genetic elements encoding virulence proteins with attenuated or enhanced activity in ruminants were widely distributed in CC133 isolates, suggesting a key role in its host-specific interactions. To investigate this further, we examined the activity of a novel staphylococcal pathogenicity island (SaPIov2) found in the great majority of CC133 isolates which encodes a variant of the chromosomally encoded von Willebrand-binding protein (vWbp(Sov2)), previously demonstrated to have coagulase activity for human plasma. Remarkably, we discovered that SaPIov2 confers the ability to coagulate ruminant plasma suggesting an important role in ruminant disease pathogenesis and revealing the origin of a defining phenotype of the classical S. aureus biotyping scheme. Taken together, these data provide broad new insights into the origin and molecular basis of S. aureus ruminant host specificity.}, author = {Guinane, Caitriona M and Ben Zakour, Nouri L and Tormo-Mas, Maria A and Weinert, Lucy A and Lowder, Bethan V and Cartwright, Robyn A and Smyth, Davida S and Smyth, Cyril J and Lindsay, Jodi A and Gould, Katherine A and Witney, Adam and Hinds, Jason and Jonathan Bollback and Rambaut, Andrew and Penades, Jose R and Fitzgerald, J Ross}, journal = {Genome Biology and Evolution}, pages = {454 -- 466}, publisher = {Oxford University Press}, title = {{Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation}}, doi = {10.1093/gbe/evq031}, volume = {2}, year = {2010}, } @inproceedings{4361, abstract = {Depth-bounded processes form the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. In this paper we develop an adequate domain of limits for the well-structured transition systems that are induced by depth-bounded processes. An immediate consequence of our result is that there exists a forward algorithm that decides the covering problem for this class. Unlike backward algorithms, the forward algorithm terminates even if the depth of the process is not known a priori. More importantly, our result suggests a whole spectrum of forward algorithms that enable the effective verification of a large class of mobile systems.}, author = {Wies, Thomas and Zufferey, Damien and Henzinger, Thomas A}, editor = {Ong, Luke}, location = {Paphos, Cyprus}, pages = {94 -- 108}, publisher = {Springer}, title = {{Forward analysis of depth-bounded processes}}, doi = {10.1007/978-3-642-12032-9_8}, volume = {6014}, year = {2010}, } @inproceedings{4362, abstract = {Software transactional memories (STMs) promise simple and efficient concurrent programming. Several correctness properties have been proposed for STMs. Based on a bounded conflict graph algorithm for verifying correctness of STMs, we develop TRACER, a tool for runtime verification of STM implementations. The novelty of TRACER lies in the way it combines coarse and precise runtime analyses to guarantee sound and complete verification in an efficient manner. We implement TRACER in the TL2 STM implementation. We evaluate the performance of TRACER on STAMP benchmarks. While a precise runtime verification technique based on conflict graphs results in an average slowdown of 60x, the two-level approach of TRACER performs complete verification with an average slowdown of around 25x across different benchmarks.}, author = {Singh, Vasu}, editor = {Sokolsky, Oleg and Rosu, Grigore and Tilmann, Nikolai and Barringer, Howard and Falcone, Ylies and Finkbeiner, Bernd and Havelund, Klaus and Lee, Insup and Pace, Gordon}, location = {St. Julians, Malta}, pages = {421 -- 435}, publisher = {Springer}, title = {{Runtime verification for software transactional memories}}, doi = {10.1007/978-3-642-16612-9_32}, volume = {6418}, year = {2010}, } @inproceedings{4364, author = {Podelski,Andreas and Thomas Wies}, pages = {249 -- 260}, publisher = {ACM}, title = {{Counterexample-guided focus}}, doi = {10.1145/1707801.1706330}, year = {2010}, } @inproceedings{4369, abstract = {In this paper we propose a novel technique for constructing timed automata from properties expressed in the logic mtl, under bounded-variability assumptions. We handle full mtl and include all future operators. Our construction is based on separation of the continuous time monitoring of the input sequence and discrete predictions regarding the future. The separation of the continuous from the discrete allows us to determinize our automata in an exponential construction that does not increase the number of clocks. This leads to a doubly exponential construction from mtl to deterministic timed automata, compared with triply exponential using existing approaches. We offer an alternative to the existing approach to linear real-time model checking, which has never been implemented. It further offers a unified framework for model checking, runtime monitoring, and synthesis, in an approach that can reuse tools, implementations, and insights from the discrete setting.}, author = {Nickovic, Dejan and Piterman, Nir}, editor = {Henzinger, Thomas A. and Chatterjee, Krishnendu}, location = {Klosterneuburg, Austria}, pages = {152 -- 167}, publisher = {Springer}, title = {{From MTL to deterministic timed automata}}, doi = {10.1007/978-3-642-15297-9_13}, volume = {6246}, year = {2010}, } @inproceedings{4378, abstract = {Techniques such as verification condition generation, predicate abstraction, and expressive type systems reduce software verification to proving formulas in expressive logics. Programs and their specifications often make use of data structures such as sets, multisets, algebraic data types, or graphs. Consequently, formulas generated from verification also involve such data structures. To automate the proofs of such formulas we propose a logic (a “calculus”) of such data structures. We build the calculus by starting from decidable logics of individual data structures, and connecting them through functions and sets, in ways that go beyond the frameworks such as Nelson-Oppen. The result are new decidable logics that can simultaneously specify properties of different kinds of data structures and overcome the limitations of the individual logics. Several of our decidable logics include abstraction functions that map a data structure into its more abstract view (a tree into a multiset, a multiset into a set), into a numerical quantity (the size or the height), or into the truth value of a candidate data structure invariant (sortedness, or the heap property). For algebraic data types, we identify an asymptotic many-to-one condition on the abstraction function that guarantees the existence of a decision procedure. In addition to the combination based on abstraction functions, we can combine multiple data structure theories if they all reduce to the same data structure logic. As an instance of this approach, we describe a decidable logic whose formulas are propositional combinations of formulas in: weak monadic second-order logic of two successors, two-variable logic with counting, multiset algebra with Presburger arithmetic, the Bernays-Schönfinkel-Ramsey class of first-order logic, and the logic of algebraic data types with the set content function. The subformulas in this combination can share common variables that refer to sets of objects along with the common set algebra operations. Such sound and complete combination is possible because the relations on sets definable in the component logics are all expressible in Boolean Algebra with Presburger Arithmetic. Presburger arithmetic and its new extensions play an important role in our decidability results. In several cases, when we combine logics that belong to NP, we can prove the satisfiability for the combined logic is still in NP.}, author = {Kuncak, Viktor and Piskac, Ruzica and Suter, Philippe and Wies, Thomas}, editor = {Barthe, Gilles and Hermenegildo, Manuel}, location = {Madrid, Spain}, pages = {26 -- 44}, publisher = {Springer}, title = {{Building a calculus of data structures}}, doi = {10.1007/978-3-642-11319-2_6}, volume = {5944}, year = {2010}, } @article{4379, abstract = {The formal specification component of verification can be exported to simulation through the idea of property checkers. The essence of this approach is the automatic construction of an observer from the specification in the form of a program that can be interfaced with a simulator and alert the user if the property is violated by a simulation trace. Although not complete, this lighter approach to formal verification has been effectively used in software and digital hardware to detect errors. Recently, the idea of property checkers has been extended to analog and mixed-signal systems. In this paper, we apply the property-based checking methodology to an industrial and realistic example of a DDR2 memory interface. The properties describing the DDR2 analog behavior are expressed in the formal specification language stl/psl in form of assertions. The simulation traces generated from an actual DDR2 interface design are checked with respect to the stl/psl assertions using the amt tool. The focus of this paper is on the translation of the official (informal and descriptive) specification of two non-trivial DDR2 properties into stl/psl assertions. We study both the benefits and the current limits of such approach. }, author = {Jones, Kevin D and Konrad,Victor and Dejan Nickovic}, journal = {Formal Methods in System Design}, number = {2}, pages = {114 -- 130}, publisher = {Springer}, title = {{Analog property checkers: a DDR2 case study}}, doi = {10.1007/s10703-009-0085-x}, volume = {36}, year = {2010}, } @inproceedings{4380, abstract = {Cloud computing is an emerging paradigm aimed to offer users pay-per-use computing resources, while leaving the burden of managing the computing infrastructure to the cloud provider. We present a new programming and pricing model that gives the cloud user the flexibility of trading execution speed and price on a per-job basis. We discuss the scheduling and resource management challenges for the cloud provider that arise in the implementation of this model. We argue that techniques from real-time and embedded software can be useful in this context.}, author = {Henzinger, Thomas A and Tomar, Anmol and Singh, Vasu and Wies, Thomas and Zufferey, Damien}, location = {Arizona, USA}, pages = {1 -- 8}, publisher = {ACM}, title = {{A marketplace for cloud resources}}, doi = {10.1145/1879021.1879022}, year = {2010}, } @inproceedings{4381, abstract = {Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We claim that, in order to realize the full potential of cloud computing, the user must be presented with a pricing model that offers flexibility at the requirements level, such as a choice between different degrees of execution speed and the cloud provider must be presented with a programming model that offers flexibility at the execution level, such as a choice between different scheduling policies. In such a flexible framework, with each job, the user purchases a virtual computer with the desired speed and cost characteristics, and the cloud provider can optimize the utilization of resources across a stream of jobs from different users. We designed a flexible framework to test our hypothesis, which is called FlexPRICE (Flexible Provisioning of Resources in a Cloud Environment) and works as follows. A user presents a job to the cloud. The cloud finds different schedules to execute the job and presents a set of quotes to the user in terms of price and duration for the execution. The user then chooses a particular quote and the cloud is obliged to execute the job according to the chosen quote. FlexPRICE thus hides the complexity of the actual scheduling decisions from the user, but still provides enough flexibility to meet the users actual demands. We implemented FlexPRICE in a simulator called PRICES that allows us to experiment with our framework. We observe that FlexPRICE provides a wide range of execution options-from fast and expensive to slow and cheap-- for the whole spectrum of data-intensive and computation-intensive jobs. We also observe that the set of quotes computed by FlexPRICE do not vary as the number of simultaneous jobs increases.}, author = {Henzinger, Thomas A and Tomar, Anmol and Singh, Vasu and Wies, Thomas and Zufferey, Damien}, location = {Miami, USA}, pages = {83 -- 90}, publisher = {IEEE}, title = {{FlexPRICE: Flexible provisioning of resources in a cloud environment}}, doi = {10.1109/CLOUD.2010.71}, year = {2010}, } @inproceedings{4382, abstract = {Transactional memory (TM) has shown potential to simplify the task of writing concurrent programs. Inspired by classical work on databases, formal definitions of the semantics of TM executions have been proposed. Many of these definitions assumed that accesses to shared data are solely performed through transactions. In practice, due to legacy code and concurrency libraries, transactions in a TM have to share data with non-transactional operations. The semantics of such interaction, while widely discussed by practitioners, lacks a clear formal specification. Those interactions can vary, sometimes in subtle ways, between TM implementations and underlying memory models. We propose a correctness condition for TMs, parametrized opacity, to formally capture the now folklore notion of strong atomicity by stipulating the two following intuitive requirements: first, every transaction appears as if it is executed instantaneously with respect to other transactions and non-transactional operations, and second, non-transactional operations conform to the given underlying memory model. We investigate the inherent cost of implementing parametrized opacity. We first prove that parametrized opacity requires either instrumenting non-transactional operations (for most memory models) or writing to memory by transactions using potentially expensive read-modify-write instructions (such as compare-and-swap). Then, we show that for a class of practical relaxed memory models, parametrized opacity can indeed be implemented with constant-time instrumentation of non-transactional writes and no instrumentation of non-transactional reads. We show that, in practice, parametrizing the notion of correctness allows developing more efficient TM implementations.}, author = {Guerraoui, Rachid and Henzinger, Thomas A and Kapalka, Michal and Singh, Vasu}, location = {Santorini, Greece}, pages = {263 -- 272}, publisher = {ACM}, title = {{Transactions in the jungle}}, doi = {10.1145/1810479.1810529}, year = {2010}, }