Functional renormalization group study of the Anderson--Holstein model

We present a comprehensive study of the spectral and transport properties in the Anderson--Holstein model both in and out of equilibrium using the functional renormalization group (FRG). We show how the previously established machinery of Matsubara and Keldysh FRG can be extended to include the local phonon mode. Based on the analysis of spectral properties in equilibrium we identify different regimes depending on the strength of the electron--phonon interaction and the frequency of the phonon mode. We supplement these considerations with analytical results from the Kondo model. We also calculate the non-linear differential conductance through the Anderson--Holstein quantum dot and find clear signatures of the presence of the phonon mode.Comment: 19 pages, 8 figure

Single Molecule Studies of Myosin-Ib

Myosin-Is are the single-headed, membrane-associated members of the myosin superfamily that are found in many eukaryotic cells. These actin-based motors have been shown to play important roles in powering membrane dynamics, defining cytoskeletal structure, and regulating mechanical signal-transduction. However, many molecular details of myosin-I function are not known. My goal has been to determine the mechanical and kinetic properties of a myosin-I isoform (myo1b) as it undergoes its force-generating power stroke under physiological tension and when external mechanical loads are applied to it. We therefore characterized the force dependence of myo1b splice isoforms using an optical trap and a novel isometric force clamp. Myo1b is alternatively spliced within the regulatory domain of the molecule, yielding motors that have “lever-arms” with different lengths. We found the actin-attachment kinetics of all myo1b splice isoforms to be highly force sensitive, with forces of \u3c 2 pN decreasing the rate of actin detachment \u3e 75 fold. However, we found that the magnitude of the tension sensitivities depend on the splice isoform. Therefore, we propose that the tension sensing properties of myo1b are transcriptionally regulated. Finally, we found the tension sensitivity of myo1b to be regulated by calcium, such that micromolar calcium concentrations effectively uncouple the myosin active site from lever arm rotation. Taken together, this work supports a model in which myosin-Is play roles in generating and sustaining membrane tension, and that the mechanochemical properties of this protein are regulated by alternative splicing and calcium

Physics of Proximity Josephson Sensor

We study the proximity Josephson sensor (PJS) in both bolometric and calorimetric operation and optimize it for different temperature ranges between 25 mK and a few Kelvin. We investigate how the radiation power is absorbed in the sensor and find that the irradiated sensor is typically in a weak nonequilibrium state. We show in detail how the proximity of the superconductors affects the device response: for example via changes in electron-phonon coupling and out-of-equilibrium noise. In addition, we estimate the applicability of graphene as the absorber material.Comment: 13 pages, 11 figures, submitted to Journal of Applied Physics, v2: Addition of a new section discussing the radiation coupling to the device, several minor change

Theory of temperature fluctuation statistics in superconductor-normal metal tunnel structures

We describe the statistics of temperature fluctuations in a SINIS structure, where a normal metal island (N) is coupled by tunnel junctions (I) to two superconducting leads (S). We specify conditions under which this structure exhibits manifestly non-Gaussian fluctuations of temperature. We consider both the Gaussian and non-Gaussian regimes of these fluctuations, and the current fluctuations that are caused by the fluctuating temperature. We also describe a measurement setup that could be used to observe the temperature fluctuations.Comment: 10 pages, 9 figures, final versio

Dali server update

The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo.Peer reviewe

Fully Overheated Single-Electron Transistor

We consider the fully overheated single-electron transistor, where the heat balance is determined entirely by electron transfers. We find three distinct transport regimes corresponding to cotunneling, single-electron tunneling, and a competition between the two. We find an anomalous sensitivity to temperature fluctuations at the crossover between the two latter regimes that manifests in an exceptionally large Fano factor of current noise.Comment: 6 pages, 3 figures, includes Appendi

Nonequilibrium characteristics in all-superconducting tunnel structures

We study the nonequilibrium characteristics of superconducting tunnel structures in the case when one of the superconductors is a small island confined between large superconductors. The state of this island can be probed for example via the supercurrent flowing through it. We study both the far-from-equilibrium limit when the rate of injection for the electrons into the island exceeds the energy relaxation inside it, and the quasiequilibrium limit when the electrons equilibrate between themselves. We also address the crossover between these limits employing the collision integral derived for the superconducting case. The clearest signatures of the nonequilibrium limit are the anomalous heating effects seen as a supercurrent suppression at low voltages, and the hysteresis at voltages close to the gap edge $2\Delta/e$, resulting from the peculiar form of the nonequilibrium distribution function.Comment: 8 pages, 10 figure

Charge transport in ballistic multiprobe graphene structures

We study the the transport properties of multiterminal ballistic graphene samples, concentrating on the conductance matrix, fluctuations and cross-correlations. Far away from Dirac point, the current is carried mostly by propagating modes and the results can be explained with the conventional semiclassical picture familiar from ray optics, where electrons propagate along a single direction before scattering or reaching the terminals. However, close to the Dirac point the transport is due to evanescent modes which do not have to follow a rectilinear path. As we show in this Letter, this property of the evanescent modes influences the conductance matrix. However, at best it can be observed by measuring the cross correlations in an exchange Hanbury Brown-Twiss experiment.Comment: 5 pages, 5 figure

The use of laptop computers in programming lectures

This research explores the effect of the use of laptop computers on students&rsquo; learning experiences during lectures. Our methodology involves embedding laptops with visualization software as a learning aid during lectures. We then employ a framework of seven principles of good practice in higher education to evaluate the impact of the use of laptop computers on the learning experience of computer programming students. Overall, we found that students were highly motivated and supportive of this innovative use of laptop computers with lectures.<br /