Small-World Rouse Networks as models of cross-linked polymers

We use the recently introduced small-world networks (SWN) to model cross-linked polymers, as an extension of the linear Rouse-chain. We study the SWN-dynamics under the influence of external forces. Our focus is on the structurally and thermally averaged SWN stretching, which we determine both numerically and analytically using a psudo-gap ansatz for the SWN-density of states. The SWN stretching is related to the probability of a random-walker to return to its origin on the SWN. We compare our results to the corresponding ones for Cayley trees.Comment: 14 pages, 4 figures. Preprint version, submitted to JC

Coupling of shells in a carbon nanotube quantum dot

We systematically study the coupling of longitudinal modes (shells) in a carbon nanotube quantum dot. Inelastic cotunneling spectroscopy is used to probe the excitation spectrum in parallel, perpendicular and rotating magnetic fields. The data is compared to a theoretical model including coupling between shells, induced by atomically sharp disorder in the nanotube. The calculated excitation spectra show good correspondence with experimental data.Comment: 8 pages, 4 figure

Tunneling Spectroscopy of Quasiparticle Bound States in a Spinful Josephson Junction

The spectrum of a segment of InAs nanowire, confined between two superconducting leads, was measured as function of gate voltage and superconducting phase difference using a third normal-metal tunnel probe. Sub-gap resonances for odd electron occupancy---interpreted as bound states involving a confined electron and a quasiparticle from the superconducting leads, reminiscent of Yu-Shiba-Rusinov states---evolve into Kondo-related resonances at higher magnetic fields. An additional zero bias peak of unknown origin is observed to coexist with the quasiparticle bound states.Comment: Supplementary information available here: https://dl.dropbox.com/u/1742676/Chang_Sup.pd

Double Diffusion Encoding Prevents Degeneracy in Parameter Estimation of Biophysical Models in Diffusion MRI

Purpose: Biophysical tissue models are increasingly used in the interpretation of diffusion MRI (dMRI) data, with the potential to provide specific biomarkers of brain microstructural changes. However, the general Standard Model has recently shown that model parameter estimation from dMRI data is ill-posed unless very strong magnetic gradients are used. We analyse this issue for the Neurite Orientation Dispersion and Density Imaging with Diffusivity Assessment (NODDIDA) model and demonstrate that its extension from Single Diffusion Encoding (SDE) to Double Diffusion Encoding (DDE) solves the ill-posedness and increases the accuracy of the parameter estimation. Methods: We analyse theoretically the cumulant expansion up to fourth order in b of SDE and DDE signals. Additionally, we perform in silico experiments to compare SDE and DDE capabilities under similar noise conditions. Results: We prove analytically that DDE provides invariant information non-accessible from SDE, which makes the NODDIDA parameter estimation injective. The in silico experiments show that DDE reduces the bias and mean square error of the estimation along the whole feasible region of 5D model parameter space. Conclusions: DDE adds additional information for estimating the model parameters, unexplored by SDE, which is enough to solve the degeneracy in the NODDIDA model parameter estimation.Comment: 22 pages, 7 figure

Small-World Networks: Links with long-tailed distributions

Small-world networks (SWN), obtained by randomly adding to a regular structure additional links (AL), are of current interest. In this article we explore (based on physical models) a new variant of SWN, in which the probability of realizing an AL depends on the chemical distance between the connected sites. We assume a power-law probability distribution and study random walkers on the network, focussing especially on their probability of being at the origin. We connect the results to L\'evy Flights, which follow from a mean field variant of our model.Comment: 11 pages, 4 figures, to appear in Phys.Rev.

CO2-Fixation Strategies in Energy Extremophiles: What Can We Learn From Acetogens?

Domestication of CO2-fixation became a worldwide priority enhanced by the will to convert this greenhouse gas into fuels and valuable chemicals. Because of its high stability, CO2-activation/fixation represents a true challenge for chemists. Autotrophic microbial communities, however, perform these reactions under standard temperature and pressure. Recent discoveries shine light on autotrophic acetogenic bacteria and hydrogenotrophic methanogens, as these anaerobes use a particularly efficient CO2-capture system to fulfill their carbon and energy needs. While other autotrophs assimilate CO2 via carboxylation followed by a reduction, acetogens and methanogens do the opposite. They first generate formate and CO by CO2-reduction, which are subsequently fixed to funnel the carbon toward their central metabolism. Yet their CO2-reduction pathways, with acetate or methane as end-products, constrain them to thrive at the "thermodynamic limits of Life". Despite this energy restriction acetogens and methanogens are growing at unexpected fast rates. To overcome the thermodynamic barrier of CO2-reduction they apply different ingenious chemical tricks such as the use of flavin-based electron-bifurcation or coupled reactions. This mini-review summarizes the current knowledge gathered on the CO2-fixation strategies among acetogens. While extensive biochemical characterization of the acetogenic formate-generating machineries has been done, there is no structural data available. Based on their shared mechanistic similarities, we apply the structural information obtained from hydrogenotrophic methanogens to highlight common features, as well as the specific differences of their CO2-fixation systems. We discuss the consequences of their CO2-reduction strategies on the evolution of Life, their wide distribution and their impact in biotechnological applications

A Semiconductor Nanowire-Based Superconducting Qubit

We introduce a hybrid qubit based on a semiconductor nanowire with an epitaxially grown superconductor layer. Josephson energy of the transmon-like device ("gatemon") is controlled by an electrostatic gate that depletes carriers in a semiconducting weak link region. Strong coupling to an on-chip microwave cavity and coherent qubit control via gate voltage pulses is demonstrated, yielding reasonably long relaxation times (0.8 {\mu}s) and dephasing times (1 {\mu}s), exceeding gate operation times by two orders of magnitude, in these first-generation devices. Because qubit control relies on voltages rather than fluxes, dissipation in resistive control lines is reduced, screening reduces crosstalk, and the absence of flux control allows operation in a magnetic field, relevant for topological quantum information

Parity lifetime of bound states in a proximitized semiconductor nanowire

Quasiparticle excitations can compromise the performance of superconducting devices, causing high frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we introduce a new physical system comprised of a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify Andreev-like bound states in the semiconductor via bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms.Comment: text and supplementary information combine

Transport signatures of quasiparticle poisoning in a Majorana island

We investigate effects of quasiparticle poisoning in a Majorana island with strong tunnel coupling to normal-metal leads. In addition to the main Coulomb blockade diamonds, "shadow" diamonds appear, shifted by 1e in gate voltage, consistent with transport through an excited (poisoned) state of the island. Comparison to a simple model yields an estimate of parity lifetime for the strongly coupled island (~ 1 {\mu}s) and sets a bound for a weakly coupled island (> 10 {\mu}s). Fluctuations in the gate-voltage spacing of Coulomb peaks at high field, reflecting Majorana hybridization, are enhanced by the reduced lever arm at strong coupling. In energy units, fluctuations are consistent with previous measurements.Comment: includes supplementary materia

Correlation effects in a simple model of small-world network

We analyze the effect of correlations in a simple model of small world network by obtaining exact analytical expressions for the distribution of shortest paths in the network. We enter correlations into a simple model with a distinguished site, by taking the random connections to this site from an Ising distribution. Our method shows how the transfer matrix technique can be used in the new context of small world networks.Comment: 10 pages, 3 figure