Phase Evolution in a Kondo Correlated System

The coherence and phase evolution of electrons in a mesoscopic system in the Kondo correlated regime were studied. The Kondo effect, in turn, is one of the most fundamental many-body effects where a localized spin interacts with conduction electrons in a conductor. Results were obtained by embedding a quantum dot (QD) in a double path electronic interferometer and measuring interference of electron waves. The Phase was found to evolve in a range twice as large as the theoretically predicted one. Moreover, the phase proved to be highly sensitive to the onset of Kondo correlation, thus serving as a new fingerprint of the Kondo effect.Comment: 4 pages, 4 figures. typos corrected. Changed to APS PRL styl

Reconstruction of Causal Networks by Set Covering

We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show that global consistency with the data can be achieved through purely local considerations, inferring the neighbourhood of each node in turn. The optimisation problem solved for each individual node can be reduced to a Set Covering Problem, which is known to be NP-hard but can be approximated well in practice. We then extend our approach to account for noisy data, based on the Minimum Description Length principle. We demonstrate our algorithms on synthetic data, generated by an SIR-like epidemiological model.Comment: Under consideration for the ECML PKDD 2010 conferenc

Scattering Theory of Mesoscopic Detectors

We consider a two-level system coupled to a mesoscopic two-terminal conductor that acts as measuring device. As a convenient description of the conductor we introduce its scattering matrix. We show how its elements can be used to calculate the relaxation and decoherence rates of the two-level system. Special emphasis is laid on the charge screening in the conductor that becomes important in the many-channel limit. Finally we give some examples that illustrate charge screening in different limits.Comment: contribution to the ECOSS-21 proceedings in a special issue of SURFACE SCIENC

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression

<p>Abstract</p> <p>Background</p> <p>Many of the functional units in cells are multi-protein complexes such as RNA polymerase, the ribosome, and the proteasome. For such units to work together, one might expect a high level of regulation to enable co-appearance or repression of sets of complexes at the required time. However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships.</p> <p>Results</p> <p>We detect coordinated regulation of multiple protein complexes using <it>logic analysis </it>of gene expression data. Specifically, we identify gene triplets composed of genes whose expression profiles are found to be related by various types of logic functions. In order to focus on complexes, we associate the members of a gene triplet with the distinct protein complexes to which they belong. In this way, we identify complexes related by specific kinds of regulatory relationships. For example, we may find that the transcription of complex C is increased only if the transcription of both complex A AND complex B is repressed. We identify hundreds of examples of coordinated regulation among complexes under various stress conditions. Many of these examples involve the ribosome. Some of our examples have been previously identified in the literature, while others are novel. One notable example is the relationship between the transcription of the ribosome, RNA polymerase and mannosyltransferase II, which is involved in N-linked glycan processing in the Golgi.</p> <p>Conclusions</p> <p>The analysis proposed here focuses on relationships among triplets of genes that are not evident when genes are examined in a pairwise fashion as in typical clustering methods. By grouping gene triplets, we are able to decipher coordinated regulation among sets of three complexes. Moreover, using all triplets that involve coordinated regulation with the ribosome, we derive a large network involving this essential cellular complex. In this network we find that all multi-protein complexes that belong to the same functional class are regulated in the same direction as a group (either induced or repressed).</p

Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states

The Notch signaling pathway consists of multiple types of receptors and ligands, whose interactions can be tuned by Fringe glycosyltransferases. A major challenge is to determine how these components control the specificity and directionality of Notch signaling in developmental contexts. Here, we analyzed same-cell (cis) Notch-ligand interactions for Notch1, Dll1, and Jag1, and their dependence on Fringe protein expression in mammalian cells. We found that Dll1 and Jag1 can cis-inhibit Notch1, and Fringe proteins modulate these interactions in a way that parallels their effects on trans interactions. Fringe similarly modulated Notch-ligand cis interactions during Drosophila development. Based on these and previously identified interactions, we show how the design of the Notch signaling pathway leads to a restricted repertoire of signaling states that promote heterotypic signaling between distinct cell types, providing insight into the design principles of the Notch signaling system, and the specific developmental process of Drosophila dorsal-ventral boundary formation

Dynamic Ligand Discrimination in the Notch Signaling Pathway

The Notch signaling pathway comprises multiple ligands that are used in distinct biological contexts. In principle, different ligands could activate distinct target programs in signal-receiving cells, but it is unclear how such ligand discrimination could occur. Here, we show that cells use dynamics to discriminate signaling by the ligands Dll1 and Dll4 through the Notch1 receptor. Quantitative single-cell imaging revealed that Dll1 activates Notch1 in discrete, frequency-modulated pulses that specifically upregulate the Notch target gene Hes1. By contrast, Dll4 activates Notch1 in a sustained, amplitude-modulated manner that predominantly upregulates Hey1 and HeyL. Ectopic expression of Dll1 or Dll4 in chick neural crest produced opposite effects on myogenic differentiation, showing that ligand discrimination can occur in vivo. Finally, analysis of chimeric ligands suggests that ligand-receptor clustering underlies dynamic encoding of ligand identity. The ability of the pathway to utilize ligands as distinct communication channels has implications for diverse Notch-dependent processes

An Electronic Mach-Zehnder Interferometer

Double-slit electron interferometers, fabricated in high mobility two-dimensional electron gas (2DEG), proved to be very powerful tools in studying coherent wave-like phenomena in mesoscopic systems. However, they suffer from small fringe visibility due to the many channels in each slit and poor sensitivity to small currents due to their open geometry. Moreover, the interferometers do not function in a high magnetic field, namely, in the quantum Hall effect (QHE) regime, since it destroys the symmetry between left and right slits. Here, we report on the fabrication and operation of a novel, single channel, two-path electron interferometer that functions in a high magnetic field. It is the first electronic analog of the well-known optical Mach-Zehnder (MZ) interferometer. Based on single edge state and closed geometry transport in the QHE regime the interferometer is highly sensitive and exhibits very high visibility (62%). However, the interference pattern decays precipitously with increasing electron temperature or energy. While we do not understand the reason for the dephasing we show, via shot noise measurement, that it is not a decoherence process that results from inelastic scattering events.Comment: to appear in Natur

Storage Qubits and Their Potential Implementation Through a Semiconductor Double Quantum Dot

In the context of a semiconductor based implementation of a quantum computer the idea of a quantum storage bit is presented and a possible implementation using a double quantum dot structure is considered. A measurement scheme using a stimulated Raman adiabatic passage is discussed.Comment: Revised version accepted for publication in Phys.Rev. B. 19 pages, 4 eps figure