@article{8477, abstract = {An optimized NMR experiment that combines the advantages of methyl-TROSY and SOFAST-HMQC has been developed. It allows the recording of high quality methyl 1H−13C correlation spectra of protein assemblies of several hundreds of kDa in a few seconds. The SOFAST-methyl-TROSY-based experiment offers completely new opportunities for the study of structural and dynamic changes occurring in molecular nanomachines while they perform their biological function in vitro.}, author = {Amero, Carlos and Schanda, Paul and Durá, M. Asunción and Ayala, Isabel and Marion, Dominique and Franzetti, Bruno and Brutscher, Bernhard and Boisbouvier, Jérôme}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {10}, pages = {3448--3449}, publisher = {American Chemical Society}, title = {{Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies}}, doi = {10.1021/ja809880p}, volume = {131}, year = {2009}, } @article{8478, abstract = {Allosteric regulation is an effective mechanism of control in biological processes. In allosteric proteins a signal originating at one site in the molecule is communicated through the protein structure to trigger a specific response at a remote site. Using NMR relaxation dispersion techniques we directly observe the dynamic process through which the KIX domain of CREB binding protein communicates allosteric information between binding sites. KIX mediates cooperativity between pairs of transcription factors through binding to two distinct interaction surfaces in an allosteric manner. We show that binding the activation domain of the mixed lineage leukemia (MLL) transcription factor to KIX induces a redistribution of the relative populations of KIX conformations toward a high-energy state in which the allosterically activated second binding site is already preformed, consistent with the Monod−Wyman−Changeux (WMC) model of allostery. The structural rearrangement process that links the two conformers and by which allosteric information is communicated occurs with a time constant of 3 ms at 27 °C. Our dynamic NMR data reveal that an evolutionarily conserved network of hydrophobic amino acids constitutes the pathway through which information is transmitted.}, author = {Brüschweiler, Sven and Schanda, Paul and Kloiber, Karin and Brutscher, Bernhard and Kontaxis, Georg and Konrat, Robert and Tollinger, Martin}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {8}, pages = {3063--3068}, publisher = {American Chemical Society}, title = {{Direct observation of the dynamic process underlying allosteric signal transmission}}, doi = {10.1021/ja809947w}, volume = {131}, year = {2009}, } @article{8479, abstract = {Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1H–15N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds.}, author = {Gal, Maayan and Kern, Thomas and Schanda, Paul and Frydman, Lucio and Brutscher, Bernhard}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, pages = {1--10}, publisher = {Springer Nature}, title = {{An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates}}, doi = {10.1007/s10858-008-9284-9}, volume = {43}, year = {2009}, } @article{8508, abstract = {We study generic unfoldings of homoclinic tangencies of two-dimensional area-preserving diffeomorphisms (conservative New house phenomena) and show that they give rise to invariant hyperbolic sets of arbitrarily large Hausdorff dimension. As applications, we discuss the size of the stochastic layer of a standard map and the Hausdorff dimension of invariant hyperbolic sets for certain restricted three-body problems. We avoid involved technical details and only concentrate on the ideas of the proof of the presented results.}, author = {Gorodetski, Anton and Kaloshin, Vadim}, issn = {0081-5438}, journal = {Proceedings of the Steklov Institute of Mathematics}, keywords = {Mathematics (miscellaneous)}, number = {1}, pages = {76--90}, publisher = {Springer Nature}, title = {{Conservative homoclinic bifurcations and some applications}}, doi = {10.1134/s0081543809040063}, volume = {267}, year = {2009}, } @article{88, abstract = {We have developed a tunable source of Mie scale microdroplet aerosols that can be used for the generation of energetic ions. To demonstrate this potential, a terawatt Ti: Al2 O3 laser focused to 2×10 19 W/cm2 was used to irradiate heavy water (D2 O) aerosols composed of micron-scale droplets. Energetic deuterium ions, which were generated in the laser-droplet interaction, produced deuterium-deuterium fusion with approximately 2×10^3 fusion neutrons measured per joule of incident laser energy. }, author = {Higginbotham, Andrew P and Semonin, Octavi and Bruce, S and Chan, C and Maindi, M and Donnelly, Tom and Maurer, M and Bang, Woosuk and Churina, I.V and Osterholz, Jens and Kim, I and Bernstein, Aaron and Ditmire, Todd}, journal = {Review of Scientific Instruments}, number = {6}, publisher = {American Institute of Physics}, title = {{Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments}}, doi = {10.1063/1.3155302}, volume = {80}, year = {2009}, } @inbook{164, abstract = {Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method.}, author = {Browning, Timothy D and Heath Brown, Roger}, booktitle = {Analytic Number Theory: Essays in honour of Klaus Roth}, pages = {75 -- 90}, publisher = {Cambridge University Press}, title = {{Integral points on cubic hypersurfaces}}, year = {2009}, } @inproceedings{165, abstract = {We survey the state of affairs for the distribution of ℚ-rational points on non-singular del Pezzo surfaces of low degree, highlighting the recent resolution of Manin's conjecture for a non-singular del Pezzo surface of degree 4 by la Bretèche and Browning.}, author = {Timothy Browning}, editor = {Aoki, Takashi and Kanemitsu, Shigeru and Liu, Jianya}, pages = {1 -- 18}, publisher = {World Scientific Publishing}, title = {{Resent progress on the quantitative arithmetic of del Pezzo surfaces}}, doi = {https://doi.org/10.1142/9789814289924_0001}, volume = {6}, year = {2009}, } @inbook{168, abstract = {The arithmetic of ternary diagonal equation is considered for degree d >1, with the outcome that the set of coefficients for which the equation admits a non-zero integer solution is shown to have density zero.}, author = {Timothy Browning and Dietmann, Rainer}, booktitle = {Quadratic Forms - algebra, arithmetic and geometry}, pages = {99 -- 106}, publisher = {American Mathematical Society}, title = {{Solubility of Fermat equations}}, doi = {http://dx.doi.org/10.1090/conm/493}, volume = {493}, year = {2009}, } @article{1718, abstract = {Morphogens act as graded positional cues to control cell fate specification in many developing tissues. This concept, in which a signaling gradient regulates differential gene expression in a concentration-dependent manner, has received considerable experimental support. Nevertheless, several recent studies have challenged the straightforward model of morphogen activity. In particular, the observation that pattern formation is a dynamic process has raised questions about the influence of time on morphogen activity. Here we propose that the spatiotemporal dynamics of the cellular response to a morphogen gradient depend on a combination of temporal alterations to the morphogen gradient itself, the dynamics of its signal transduction and downstream interactions between target genes.}, author = {Kutějová, Eva and Briscoe, James and Anna Kicheva}, journal = {Current Opinion in Genetics & Development}, number = {4}, pages = {315 -- 322}, publisher = {Elsevier}, title = {{Temporal dynamics of patterning by morphogen gradients}}, doi = {10.1016/j.gde.2009.05.004}, volume = {19}, year = {2009}, } @article{1720, abstract = {How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis.}, author = {Wartlick, Ortrud and Anna Kicheva and González-Gaitán, Marcos A}, journal = {Cold Spring Harbor perspectives in biology}, number = {3}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Morphogen gradient formation }}, doi = {10.1101/cshperspect.a001255}, volume = {1}, year = {2009}, } @article{1766, abstract = {We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation.}, author = {Leek, Peter J and Filipp, Stefan and Maurer, Patrick and Baur, Matthias P and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Wallraff, Andreas}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {18}, publisher = {American Physical Society}, title = {{Using sideband transitions for two-qubit operations in superconducting circuits}}, doi = {10.1103/PhysRevB.79.180511}, volume = {79}, year = {2009}, } @article{1767, abstract = {We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives.}, author = {Baur, Matthias P and Filipp, Stefan and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {24}, publisher = {American Physical Society}, title = {{Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit}}, doi = {10.1103/PhysRevLett.102.243602}, volume = {102}, year = {2009}, } @article{1768, abstract = {Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states.}, author = {Filipp, Stefan and Maurer, Patrick and Leek, Peter J and Baur, Matthias P and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Gambetta, Jay M and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Two-qubit state tomography using a joint dispersive readout}}, doi = {10.1103/PhysRevLett.102.200402}, volume = {102}, year = {2009}, } @article{1769, abstract = {We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers.}, author = {Johannes Fink and Bianchetti, R and Baur, Matthias P and Göppl, M and Steffen, L. Kraig and Filipp, Stefan and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Dressed collective qubit states and the Tavis-Cummings model in circuit QED}}, doi = {10.1103/PhysRevLett.103.083601}, volume = {103}, year = {2009}, } @article{1770, abstract = {The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.}, author = {Bianchetti, R and Filipp, Stefan and Baur, Matthias P and Johannes Fink and Göppl, M and Leek, Peter J and Steffen, L. Kraig and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics}}, doi = {10.1103/PhysRevA.80.043840}, volume = {80}, year = {2009}, } @article{1771, abstract = {The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits.}, author = {Johannes Fink and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Göppl, M and Leek, Peter J and Steffen, L. Kraig and Blais, Alexandre and Wallraff, Andreas}, journal = {Physica Scripta T}, publisher = {IOP Publishing Ltd.}, title = {{Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics}}, doi = {10.1088/0031-8949/2009/T137/014013}, volume = {T137}, year = {2009}, } @article{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}, }