@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{1798, abstract = {The mammalian brain is assembled from thousands of neuronal cell types that are organized in distinct circuits to perform behaviorally relevant computations. Transgenic mouse lines with selectively marked cell types would facilitate our ability to dissect functional components of complex circuits. We carried out a screen for cell type-specific green fluorescent protein expression in the retina using BAC transgenic mice from the GENSAT project. Among others, we identified mouse lines in which the inhibitory cell types of the night vision and directional selective circuit were selectively labeled. We quantified the stratification patterns to predict potential synaptic connectivity between marked cells of different lines and found that some of the lines enabled targeted recordings and imaging of cell types from developing or mature retinal circuits. Our results suggest the potential use of a stratification-based screening approach for characterizing neuronal circuitry in other layered brain structures, such as the neocortex.}, author = {Sandra Siegert and Scherf, Brigitte G and Del Punta, Karina and Didkovsky, Nick and Heintz, Nathaniel M and Roska, Botond M}, journal = {Nature Neuroscience}, number = {9}, pages = {1197 -- 1204}, publisher = {Nature Publishing Group}, title = {{Genetic address book for retinal cell types}}, doi = {10.1038/nn.2370}, volume = {12}, year = {2009}, } @article{1799, abstract = {The detection of approaching objects, such as looming predators, is necessary for survival. Which neurons and circuits mediate this function? We combined genetic labeling of cell types, two-photon microscopy, electrophysiology and theoretical modeling to address this question. We identify an approach-sensitive ganglion cell type in the mouse retina, resolve elements of its afferent neural circuit, and describe how these confer approach sensitivity on the ganglion cell. The circuit's essential building block is a rapid inhibitory pathway: it selectively suppresses responses to non-approaching objects. This rapid inhibitory pathway, which includes AII amacrine cells connected to bipolar cells through electrical synapses, was previously described in the context of night-time vision. In the daytime conditions of our experiments, the same pathway conveys signals in the reverse direction. The dual use of a neural pathway in different physiological conditions illustrates the efficiency with which several functions can be accommodated in a single circuit.}, author = {Münch, Thomas A and Da Silveira, Ravá A and Sandra Siegert and Viney, Tim J and Awatramani, Gautam B and Roska, Botond M}, journal = {Nature Neuroscience}, number = {10}, pages = {1308 -- 1316}, publisher = {Nature Publishing Group}, title = {{Approach sensitivity in the retina processed by a multifunctional neural circuit}}, doi = {10.1038/nn.2389}, volume = {12}, 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}, } @article{1971, abstract = {Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several α-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.}, author = {Berrisford, John M and Leonid Sazanov}, journal = {Journal of Biological Chemistry}, number = {43}, pages = {29773 -- 29783}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Structural basis for the mechanism of respiratory complex I}}, doi = {10.1074/jbc.M109.032144}, volume = {284}, year = {2009}, } @article{1983, abstract = {During many cellular processes such as cell division, polarization and motility, the plasma membrane does not only represent a passive physical barrier, but also provides a highly dynamic platform for the interplay between lipids, membrane binding proteins and cytoskeletal elements. Even though many regulators of these interactions are known, their mutual interdependence appears to be highly complex and difficult to study in a living cell. Over the past few years, in vitro studies on membrane-cytoskeleton interactions using biomimetic membranes turned out to be extremely helpful to get better mechanistic insight into the dynamics of these processes. In this review, we discuss some of the recent developments using in vitro assays to dissect the role of the players involved: lipids in the membrane, proteins binding to membranes and proteins binding to membrane proteins. We also summarize advantages and disadvantages of supported lipid bilayers as model membrane.}, author = {Martin Loose and Schwille, Petra }, journal = {Journal of Structural Biology}, number = {1}, pages = {143 -- 151}, publisher = {Academic Press}, title = {{Biomimetic membrane systems to study cellular organization}}, doi = {10.1016/j.jsb.2009.03.016}, volume = {168}, year = {2009}, } @article{1984, abstract = {In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14-18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.}, author = {Dinarina, Ana and Pugieux, Céline and Corral, Maria M and Martin Loose and Spatz, Joachim P and Karsenti, Éric and Nédélec, François J}, journal = {Cell}, number = {3}, pages = {502 -- 513}, publisher = {Cell Press}, title = {{Chromatin shapes the mitotic spindle}}, doi = {10.1016/j.cell.2009.05.027}, volume = {138}, year = {2009}, } @article{2067, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Genetics}, number = {4}, pages = {1699 -- 1701}, publisher = {Genetics Society of America}, title = {{Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster}}, doi = {10.1534/genetics.108.098004}, volume = {181}, year = {2009}, } @article{2068, abstract = {In Drosophila, there is a consistent deficit of male-biased genes on the X chromosome. It has been suggested that male-biased genes may evolve from initially unbiased genes as a result of increased expression levels in males. If transcription rates are limited, a large increase in expression in the testis may be harder to achieve for single-copy X-linked genes than for autosomal genes, because they are already hypertranscribed due to dosage compensation. This hypothesis predicts that the larger the increase in expression required to make a male-biased gene, the lower the chance of this being achievable if it is located on the X chromosome. Consequently, highly expressed male-biased genes should be located on the X chromosome less often than lowly expressed male-biased genes. This pattern is observed in our analysis of publicly available data, where microarray data or EST data are used to detect male-biased genes in D. melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome.}, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Journal of Molecular Evolution}, number = {5}, pages = {576 -- 583}, publisher = {Springer}, title = {{The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation?}}, doi = {10.1007/s00239-009-9235-4}, volume = {68}, year = {2009}, } @article{2069, abstract = {Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (NeX) is equal to three-quarters of the autosomal population size (NeA). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that NeX/NeA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when NeX/N eA > 3/4. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution.}, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Evolution}, number = {9}, pages = {2413 -- 2426}, publisher = {Wiley-Blackwell}, title = {{Effective population size and the faster-X effect: An extended model}}, doi = {10.1111/j.1558-5646.2009.00719.x}, volume = {63}, year = {2009}, } @article{13414, abstract = {Supraspherical aggregates of crosslinked metal nanoparticles are transformed into pancakes and nanorods by mechanical stresses and shears imparted by macroscopic objects (see image). The dimensions of both types of nanostructures can be controlled by the pressures applied.}, author = {Browne, Kevin P. and Klajn, Rafal and Villa, JulieAnn and Grzybowski, Bartosz A.}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {23}, pages = {2656--2658}, publisher = {Wiley}, title = {{Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates}}, doi = {10.1002/smll.200900902}, volume = {5}, year = {2009}, } @article{13415, abstract = {Systems in which nanoscale components of different types can be captured and/or released from organic scaffolds provide a fertile basis for the construction of dynamic, exchangeable functional materials. In such heterogeneous systems, the components interact with one another by means of programmable, noncovalent bonding interactions. Herein, we describe polymers that capture and release functionalized nanoparticles selectively during redox-controlled aggregation and disaggregation, respectively. The interactions between the polymer and the NPs are mediated by the reversible formation of polypseudorotaxanes, and give rise to architectures ranging from short chains composed of few nanoparticles to extended networks of nanoparticles crosslinked by the polymer. In the latter case, the polymer/nanoparticle aggregates precipitate from solution such that the polymer acts as a selective ‘sponge’ for the capture/release of the nanoparticles of different types.}, author = {Klajn, Rafal and Olson, Mark A. and Wesson, Paul J. and Fang, Lei and Coskun, Ali and Trabolsi, Ali and Soh, Siowling and Stoddart, J. Fraser and Grzybowski, Bartosz A.}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {General Chemical Engineering, General Chemistry}, pages = {733--738}, publisher = {Springer Nature}, title = {{Dynamic hook-and-eye nanoparticle sponges}}, doi = {10.1038/nchem.432}, volume = {1}, year = {2009}, } @article{13416, abstract = {The reversible molecular template-directed self-assembly of gold nanoparticles (AuNPs), a process which relies solely on noncovalent bonding interactions, has been demonstrated by high-resolution transmission electron microscopy (HR-TEM). By employing a well-known host−guest binding motif, the AuNPs have been systemized into discrete dimers, trimers, and tetramers. These nanoparticulate twins, triplets, and quadruplets, which can be disassembled and reassembled either chemically or electrochemically, can be coalesced into larger, permanent polygonal structures by thermal treatment using a focused HR-TEM electron beam.}, author = {Olson, Mark A. and Coskun, Ali and Klajn, Rafal and Fang, Lei and Dey, Sanjeev K. and Browne, Kevin P. and Grzybowski, Bartosz A. and Stoddart, J. Fraser}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering}, number = {9}, pages = {3185--3190}, publisher = {American Chemical Society}, title = {{Assembly of polygonal nanoparticle clusters directed by reversible noncovalent bonding interactions}}, doi = {10.1021/nl901385c}, volume = {9}, year = {2009}, } @article{13417, abstract = {Mission Impossible: Metal nanoparticles (NPs) coated with photoresponsive ligands are used as “inks” for self-erasing “paper” whereby light-induced self-assembly of the NPs is transduced into local color changes (see picture). Depending on the degree of self-assembly, multicolor images can be written using only one type of NP ink. Duration of image erasure is regulated by the surface concentration of photoactive groups and can range from seconds to days.}, author = {Klajn, Rafal and Wesson, Paul J. and Bishop, Kyle J. M. and Grzybowski, Bartosz A.}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {38}, pages = {7035--7039}, publisher = {Wiley}, title = {{Writing self-erasing images using metastable nanoparticle “inks”}}, doi = {10.1002/anie.200901119}, volume = {48}, year = {2009}, } @article{13418, abstract = {In traditional photoconductors1,2,3, the impinging light generates mobile charge carriers in the valence and/or conduction bands, causing the material’s conductivity to increase4. Such positive photoconductance is observed in both bulk and nanostructured5,6 photoconductors. Here we describe a class of nanoparticle-based materials whose conductivity can either increase or decrease on irradiation with visible light of wavelengths close to the particles’ surface plasmon resonance. The remarkable feature of these plasmonic materials is that the sign of the conductivity change and the nature of the electron transport between the nanoparticles depend on the molecules comprising the self-assembled monolayers (SAMs)7,8 stabilizing the nanoparticles. For SAMs made of electrically neutral (polar and non-polar) molecules, conductivity increases on irradiation. If, however, the SAMs contain electrically charged (either negatively or positively) groups, conductivity decreases. The optical and electrical characteristics of these previously undescribed inverse photoconductors can be engineered flexibly by adjusting the material properties of the nanoparticles and of the coating SAMs. In particular, in films comprising mixtures of different nanoparticles or nanoparticles coated with mixed SAMs, the overall photoconductance is a weighted average of the changes induced by the individual components. These and other observations can be rationalized in terms of light-induced creation of mobile charge carriers whose transport through the charged SAMs is inhibited by carrier trapping in transient polaron-like states9,10. The nanoparticle-based photoconductors we describe could have uses in chemical sensors and/or in conjunction with flexible substrates.}, author = {Nakanishi, Hideyuki and Bishop, Kyle J. M. and Kowalczyk, Bartlomiej and Nitzan, Abraham and Weiss, Emily A. and Tretiakov, Konstantin V. and Apodaca, Mario M. and Klajn, Rafal and Stoddart, J. Fraser and Grzybowski, Bartosz A.}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7253}, pages = {371--375}, publisher = {Springer Nature}, title = {{Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles}}, doi = {10.1038/nature08131}, volume = {460}, year = {2009}, } @article{13419, abstract = {Reaction-diffusion (RD) processes initiated from the surfaces of mesoscopic particles can fabricate complex core-and-shell structures. The propagation of a sharp RD front selectively removes metal colloids or nanoparticles from the supporting gel or polymer matrix. Once fabricated, the core structures can be processed “remotely” via galvanic replacement reactions, and the composite particles can be assembled into open-lattice crystals.}, author = {Wesson, Paul J. and Soh, Siowling and Klajn, Rafal and Bishop, Kyle J. M. and Gray, Timothy P. and Grzybowski, Bartosz A.}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {19}, pages = {1911--1915}, publisher = {Wiley}, title = {{“Remote” fabrication via three-dimensional reaction-diffusion: Making complex core-and-shell particles and assembling them into open-lattice crystals}}, doi = {10.1002/adma.200802964}, volume = {21}, year = {2009}, } @article{13420, abstract = {Weakly protected metal nanoparticles (MNPs) are used as precursors for the preparation of catenane- and pseudorotaxane-decorated NPs of various compositions (gold, palladium, platinum). When attached to the surface of MNPs, the molecular switches retain their switching abilities. The redox potentials of these switches depend on and can be regulated by the composition of the mixed self-assembled monolayers covering the MNPs.}, author = {Klajn, Rafal and Fang, Lei and Coskun, Ali and Olson, Mark A. and Wesson, Paul J. and Stoddart, J. Fraser and Grzybowski, Bartosz A.}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {12}, pages = {4233--4235}, publisher = {American Chemical Society}, title = {{Metal nanoparticles functionalized with molecular and supramolecular switches}}, doi = {10.1021/ja9001585}, volume = {131}, year = {2009}, }