@article{13428, abstract = {Mixtures of oppositely charged nanoparticles of various sizes and charge ratios precipitate only at the point of electroneutrality. This phenomenonspecific to the nanoscale and reminiscent of threshold precipitation of ionsis a consequence of the formation of core-and-shell nanoparticle aggregates, in which the shells are composed of like-charged particles and are stabilized by efficient electrostatic screening.}, author = {Kalsin, Alexander M. and Kowalczyk, Bartlomiej and Smoukov, Stoyan K. and Klajn, Rafal and Grzybowski, Bartosz A.}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {47}, pages = {15046--15047}, publisher = {American Chemical Society}, title = {{Ionic-like behavior of oppositely charged nanoparticles}}, doi = {10.1021/ja0642966}, volume = {128}, year = {2006}, } @article{13429, abstract = {The fruitful core: Organic syntheses reported in the literature from 1850 to 2004 are analyzed with mathematical tools from network theory and statistical physics. There is a set of substances (the core) from which the majority of other organic compounds can be made (see picture; red: core, blue: periphery, green: islands). Search algorithms are used to identify small optimal sets of maximally useful chemicals.}, author = {Bishop, Kyle J. M. and Klajn, Rafal and Grzybowski, Bartosz A.}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {32}, pages = {5348--5354}, publisher = {Wiley}, title = {{The core and most useful molecules in organic chemistry}}, doi = {10.1002/anie.200600881}, volume = {45}, year = {2006}, } @article{13430, abstract = {Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed.}, author = {Fialkowski, Marcin and Bishop, Kyle J. M. and Klajn, Rafal and Smoukov, Stoyan K. and Campbell, Christopher J. and Grzybowski, Bartosz A.}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, keywords = {Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry}, number = {6}, pages = {2482--2496}, publisher = {American Chemical Society}, title = {{Principles and implementations of dissipative (dynamic) self-assembly}}, doi = {10.1021/jp054153q}, volume = {110}, year = {2006}, } @article{1461, abstract = {This note proves combinatorially that the intersection pairing on the middle-dimensional compactly supported cohomology of a toric hyperkähler variety is always definite, providing a large number of non-trivial L 2 harmonic forms for toric hyperkähler metrics on these varieties. This is motivated by a result of Hitchin about the definiteness of the pairing of L 2 harmonic forms on complete hyperkähler manifolds of linear growth.}, author = {Tamas Hausel and Swartz, Edward}, journal = {Proceedings of the American Mathematical Society}, number = {8}, pages = {2403 -- 2409}, publisher = {American Mathematical Society}, title = {{Intersection forms of toric hyperkähler varieties}}, doi = {10.1090/S0002-9939-06-08248-7}, volume = {134}, year = {2006}, } @article{1462, abstract = {A Fourier transform technique is introduced for counting the number of solutions of holomorphic moment map equations over a finite field. This technique in turn gives information on Betti numbers of holomorphic symplectic quotients. As a consequence, simple unified proofs are obtained for formulas of Poincaré polynomials of toric hyperkähler varieties (recovering results of Bielawski-Dancer and Hausel-Sturmfels), Poincaré polynomials of Hubert schemes of points and twisted Atiyah-Drinfeld-Hitchin-Manin (ADHM) spaces of instantons on ℂ2 (recovering results of Nakajima-Yoshioka), and Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof of a conjecture of Kac on the number of absolutely indecomposable representations of a quiver is announced.}, author = {Tamas Hausel}, journal = {PNAS}, number = {16}, pages = {6120 -- 6124}, publisher = {National Academy of Sciences}, title = {{Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform}}, doi = {10.1073/pnas.0601337103}, volume = {103}, year = {2006}, } @article{1715, abstract = {Background: Cell-to-cell communication at the synapse involves synaptic transmission as well as signaling mediated by growth factors, which provide developmental and plasticity cues. There is evidence that a retrograde, presynaptic transforming growth factor-β (TGF-β) signaling event regulates synapse development and function in Drosophila. Results: Here we show that a postsynaptic TGF-β signaling event occurs during larval development. The type I receptor Thick veins (Tkv) and the R-Smad transcription factor Mothers-against-dpp (Mad) are localized postsynaptically in the muscle. Furthermore, Mad phosphorylation occurs in regions facing the presynaptic active zones of neurotransmitter release within the postsynaptic subsynaptic reticulum (SSR). In order to monitor in real time the levels of TGF-β signaling in the synapse during synaptic transmission, we have established a FRAP assay to measure Mad nuclear import/export in the muscle. We show that Mad nuclear trafficking depends on stimulation of the muscle. Conclusions: Our data suggest a mechanism linking synaptic transmission and postsynaptic TGF-β signaling that may coordinate nerve-muscle development and function.}, author = {Dudu, Veronika and Bittig, Thomas and Entchev, Eugeni and Kicheva, Anna and Julicher, Frank and González Gaitán, Marcos}, journal = {Current Biology}, number = {7}, pages = {625 -- 635}, publisher = {Cell Press}, title = {{Postsynaptic mad signaling at the Drosophila neuromuscular junction}}, doi = {10.1016/j.cub.2006.02.061}, volume = {16}, year = {2006}, } @inproceedings{18730, abstract = {We present a robust method to derive the duty cycle of QSO activity based on the empirical QSO luminosity function and on the present-day linear relation between the masses of supermassive black holes and those of their spheroidal host stellar systems. It is found that the duty cycle is substantially less than unity, with characteristic values in the range 3-6 x 10-3. Finally, we tested the expectation that the QSO luminosity evolution and the star formation history should be roughly parallel, as a consequence of the above-mentioned relation between BH and galaxy masses.}, author = {Ciotti, Luca and Haiman, Zoltán and Ostriker, Jeremiah P.}, booktitle = {Proceedings of the European Southern Observatory and Universitäts-Sternwarte München Workshop}, isbn = {9783540002055}, issn = {1611-6143}, location = {Venice, Italy}, pages = {106--108}, publisher = {Springer Nature}, title = {{What does the local black hole mass distribution tell us about the evolution of the quasar luminosity function?}}, doi = {10.1007/10899892_25}, year = {2006}, } @inproceedings{18731, abstract = {The first galaxies formed at high redshifts, and were likely substantially less massive than typical galaxies in the local universe. We argue that (1) the reionization of a clumpy intergalactic medium by redshift z=6, (2) its enrichment by metals by z=3 without disturbing the Lyman alpha forest, and (3) the presence of supermassive black holes powering the recently discovered bright quasars at z=6, strongly suggest that a population of low-mass galaxies exists beyond redshifts z>6. Although the first stars could have been born in dark matter halos with virial temperatures as low as Tvir=200K, collapsing as early as z=25, the first galaxies likely appeared in significant numbers only in halos with Tvir>10,000K that collapsed later (z=15). The gas in these more massive halos initially contracts isothermally to high densities by atomic Lyman alpha cooling. H2 molecules can then form efficiently via non-equilibrium gas-phase chemistry, allowing the gas to cool further to T=100K, and fragment on stellar mass scales. These halos can harbor the first generation of ``mini-galaxies'' that reionized the universe. The continuum and line emission from these sources, as well as their Lyman alpha cooling radiation, can be detected in the future by NGST and other instruments.}, author = {Haiman, Zoltán}, booktitle = {Proceedings of the European Southern Observatory and Universitäts-Sternwarte München Workshop}, isbn = {9783540002055}, issn = {1611-6143}, location = {Venice, Italy}, pages = {316--323}, publisher = {Springer Nature}, title = {{The assembly of the first galaxies}}, doi = {10.1007/10899892_77}, year = {2006}, } @article{1961, abstract = {Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster Nia, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex. }, author = {Leonid Sazanov and Hinchliffe, Philip }, journal = {Science}, number = {5766}, pages = {1430 -- 1436}, publisher = {American Association for the Advancement of Science}, title = {{Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus}}, doi = {10.1126/science.1123809}, volume = {311}, year = {2006}, } @article{1966, abstract = {The hydrophilic domain (peripheral arm) of the proton-translocating NADH:quinone oxidoreductase (complex I) from the thermophilic organism Thermus thermophilus HB8 has been purified and characterized. The subcomplex is stable in sodium dodecyl sulfate up to 80 °C. Of nine iron-sulfur clusters, four to five (one or two binuclear and three tetranuclear) could be detected by EPR in the NADH-reduced enzyme. The preparation consists of eight different polypeptides. Seven of them have been positively identified by peptide mass mapping and N-terminal sequencing as known hydrophilic subunits of T. thermophilus complex I. The eighth polypeptide copurified with the subcomplex at all stages, is strongly associated with the other subunits, and is present in crystals of the subcomplex, used for X-ray data collection. Therefore, it has been identified as a novel complex I subunit and named Nqo15. It is encoded in a locus separate from the nqo operon, containing the 14 other known complex I genes. ORFs encoding Nqo15 homologues are present in the genomes of the closest relatives of T. thermophilus. Our data show that, contrary to previous assumptions, bacterial complex I can contain proteins in addition to a "core" complement of 14 subunits.}, author = {Hinchliffe, Philip and Carroll, Joe D and Leonid Sazanov}, journal = {Biochemistry}, number = {14}, pages = {4413 -- 4420}, publisher = {ACS}, title = {{Identification of a novel subunit of respiratory complex I from Thermus thermophilus}}, doi = {10.1021/bi0600998}, volume = {45}, year = {2006}, } @article{4345, abstract = {Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert.}, author = {Danowski, Patrick and Heller, Lambert}, journal = {Bibliotheksdienst}, number = {11}, pages = {1250 -- 1271}, publisher = {De Gruyter}, title = {{Bibliothek 2.0 - Die Bibliothek der Zukunft?}}, doi = {10.1515/bd.2006.40.11.1259}, volume = {40}, year = {2006}, } @inproceedings{4359, abstract = {We introduce field constraint analysis, a new technique for verifying data structure invariants. A field constraint for a field is a formula specifying a set of objects to which the field can point. Field constraints enable the application of decidable logics to data structures which were originally beyond the scope of these logics, by verifying the backbone of the data structure and then verifying constraints on fields that cross-cut the backbone in arbitrary ways. Previously, such cross-cutting fields could only be verified when they were uniquely determined by the backbone, which significantly limits the range of analyzable data structures. Field constraint analysis permits non-deterministic field constraints on cross-cutting fields, which allows the verificiation of invariants for data structures such as skip lists. Non-deterministic field constraints also enable the verification of invariants between data structures, yielding an expressive generalization of static type declarations. The generality of our field constraints requires new techniques. We present one such technique and prove its soundness. We have implemented this technique as part of a symbolic shape analysis deployed in the context of the Hob system for verifying data structure consistency. Using this implementation we were able to verify data structures that were previously beyond the reach of similar techniques.}, author = {Wies, Thomas and Kuncak, Viktor and Lam, Patrick and Podelski, Andreas and Rinard, Martin}, booktitle = {7th International Conference on Verification, Model Checking, and Abstract Interpretation}, location = {Charleston, SC, United States}, pages = {157 -- 173}, publisher = {Springer}, title = {{Field constraint analysis}}, doi = {10.1007/11609773_11}, volume = {3855}, year = {2006}, } @inproceedings{4373, abstract = {This paper attempts to improve our understanding of timed languages and their relation to timed automata. We start by giving a constructive proof of the folk theorem stating that timed languages specified by the past fragment of mitl, can be accepted by deterministic timed automata. On the other hand we provide a proof that certain languages expressed in the future fragment of mitl are not deterministic, and analyze the reason for this asymmetry.}, author = {Maler, Oded and Nickovic, Dejan and Pnueli, Amir}, booktitle = {Third International Conference on Formal Modeling and Analysis of Timed Systems}, location = {Uppsala, Sweden}, pages = {2 -- 16}, publisher = {Springer}, title = {{Real time temporal logic: Past, present, future}}, doi = {10.1007/11603009_2}, volume = {3829}, year = {2006}, } @inproceedings{4374, abstract = {We show how to transform formulae written in the real-time temporal logic MITL into timed automata that recognize their satisfying models. This compositional construction is much simpler than previously known and can be easily implemented.}, author = {Maler, Oded and Nickovic, Dejan and Pnueli, Amir}, booktitle = {4th International Conference on Formal Modeling and Analysis of Timed Systems}, location = {Paris, France}, pages = {274 -- 289}, publisher = {Springer}, title = {{From MITL to timed automata}}, doi = {10.1007/11867340_20}, volume = {4202}, year = {2006}, } @inproceedings{4401, abstract = {We propose a general framework of secrecy and preservation of secrecy for labeled transition systems. Our definition of secrecy is parameterized by the distinguishing power of the observer, the properties to be kept secret, and the executions of interest, and captures a multitude of definitions in the literature. We define a notion of secrecy preserving refinement between systems by strengthening the classical trace-based refinement so that the implementation leaks a secret only when the specification also leaks it. We show that secrecy is in general not definable in μ-calculus, and thus not expressible in specification logics supported by standard model-checkers. However, we develop a simulation-based proof technique for establishing secrecy preserving refinement. This result shows how existing refinement checkers can be used to show correctness of an implementation with respect to a specification.}, author = {Alur, Rajeev and Cerny, Pavol and Zdancewic, Steve}, booktitle = {33rd International Colloquium on Automata, Languages and Programming}, pages = {107 -- 118}, publisher = {Springer}, title = {{Preserving secrecy under refinement}}, doi = {10.1007/11787006_10}, volume = {4052}, year = {2006}, } @unpublished{573, abstract = {Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol.}, author = {Hosten, Onur and Rakher, Matthew and Barreiro, Julio and Peters, Nicholas and Kwiat, Paul}, pages = {12}, publisher = {ArXiv}, title = {{Counterfactual computation revisited}}, doi = {10.48550/arXiv.quant-ph/0607101}, year = {2006}, } @unpublished{574, abstract = {Vaidman, in a recent article adopts the method of 'quantum weak measurements in pre- and postselected ensembles' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted. }, author = {Hosten, Onur and Kwiat, Paul}, pages = {2}, publisher = {ArXiv}, title = {{Weak measurements and counterfactual computation}}, doi = {10.48550/arXiv.quant-ph/0612159}, year = {2006}, } @inproceedings{577, abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio.}, author = {Rangarajan, Radhika and Altepeter, Joseph and Jeffrey, Evan and Stoutimore, Micah and Peters, Nicholas and Hosten, Onur and Kwiat, Paul}, booktitle = {Optics East}, issn = {0277-786X}, location = {Boston, Massachusetts, United States}, publisher = {SPIE}, title = {{High-efficiency single-photon detectors}}, doi = {10.1117/12.686117}, year = {2006}, } @inproceedings{578, abstract = {A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control.}, author = {Peters, Nicholas and Arnold, Keith and Vandevender, Aaron and Jeffrey, Evan and Rangarajan, Radhika and Hosten, Onur and Barreiro, Julio and Altepeter, Joseph and Kwiat, Paul}, booktitle = {Quantum Communications and Quantum Imaging IV}, location = {San DIego, CA, United States}, publisher = {SPIE}, title = {{Towards a quasi-deterministic single-photon source}}, doi = {10.1117/12.684702}, volume = {6305}, year = {2006}, } @article{579, abstract = {The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of 'running' and 'not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel 'chained' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. }, author = {Hosten, Onur and Rakher, Matthew and Barreiro, Julio and Peters, Nicholas and Kwiat, Paul}, issn = {1476-4687}, journal = {Nature}, number = {7079}, pages = {949 -- 952}, publisher = {Nature Publishing Group}, title = {{Counterfactual quantum computation through quantum interrogation}}, doi = {10.1038/nature04523}, volume = {439}, year = {2006}, }