Noise of supercontinuum sources in spectral domain optical coherence tomography

In this paper, we investigate the effect of pulse-to-pulse fluctuations of super continuum sources on the noise in spectral domain optical coherence tomography (OCT) images. The commonly quoted theoretical expression for the OCT noise is derived for a thermal light source, which is not suitable if a super continuum light source is used. We therefore propose a new, measurement-based OCT noise model that predicts the noise without any assumptions on the type of light source. We show that the predicted noise values are in excellent agreement with the measured values. The spectral correlation evaluated for the photo detected signal when using a supercontinuum determines the shape of the OCT noise floor, which must be taken into account when characterising the sensitivity roll-off of a supercontinuum-based OCT system. The spectral correlations using both conventional supercontinuum sources and low-noise all-normal dispersion super continuum sources are investigated, and the fundamental physical effects that cause these correlations are discussed

Interacting Random Walkers and Non-Equilibrium Fluctuations

We introduce a model of interacting Random Walk, whose hopping amplitude depends on the number of walkers/particles on the link. The mesoscopic counterpart of such a microscopic dynamics is a diffusing system whose diffusivity depends on the particle density. A non-equilibrium stationary flux can be induced by suitable boundary conditions, and we show indeed that it is mesoscopically described by a Fourier equation with a density dependent diffusivity. A simple mean-field description predicts a critical diffusivity if the hopping amplitude vanishes for a certain walker density. Actually, we evidence that, even if the density equals this pseudo-critical value, the system does not present any criticality but only a dynamical slowing down. This property is confirmed by the fact that, in spite of interaction, the particle distribution at equilibrium is simply described in terms of a product of Poissonians. For mesoscopic systems with a stationary flux, a very effect of interaction among particles consists in the amplification of fluctuations, which is especially relevant close to the pseudo-critical density. This agrees with analogous results obtained for Ising models, clarifying that larger fluctuations are induced by the dynamical slowing down and not by a genuine criticality. The consistency of this amplification effect with altered coloured noise in time series is also proved.Comment: 8 pages, 7 figure

The Planetary Nebula Luminosity Function at the Dawn of Gaia

The [O III] 5007 Planetary Nebula Luminosity Function (PNLF) is an excellent extragalactic standard candle. In theory, the PNLF method should not work at all, since the luminosities of the brightest planetary nebulae (PNe) should be highly sensitive to the age of their host stellar population. Yet the method appears robust, as it consistently produces < 10% distances to galaxies of all Hubble types, from the earliest ellipticals to the latest-type spirals and irregulars. It is therefore uniquely suited for cross-checking the results of other techniques and finding small offsets between the Population I and Population II distance ladders. We review the calibration of the method and show that the zero points provided by Cepheids and the Tip of the Red Giant Branch are in excellent agreement. We then compare the results of the PNLF with those from Surface Brightness Fluctuation measurements, and show that, although both techniques agree in a relative sense, the latter method yields distances that are ~15% larger than those from the PNLF. We trace this discrepancy back to the calibration galaxies and argue that, due to a small systematic error associated with internal reddening, the true distance scale likely falls between the extremes of the two methods. We also demonstrate how PNLF measurements in the early-type galaxies that have hosted Type Ia supernovae can help calibrate the SN Ia maximum magnitude-rate of decline relation. Finally, we discuss how the results from space missions such as Kepler and Gaia can help our understanding of the PNLF phenomenon and improve our knowledge of the physics of local planetary nebulae.Comment: 12 pages, invited review at the conference "The Fundamental Cosmic Distance Scale: State of the Art and Gaia Perspective", to appear in Astrophysics and Space Scienc

Discovery, characterization and engineering of bacterial thermostable cellulose- degrading enzymes

Lignocellulose is the most abundant biomass on Earth, and thus our largest organic carbon reservoir. Enzymatic depolymerization of recalcitrant polysaccharides, notably cellulose, is a major cost driver in accessing the renewable energy stored within lignocellulosic biomass. Natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. We are studying novel enzymes from various biodiversities for the conversion of lignocellulosic materials, using (meta)genome mining and functional screening of fosmid libraries. Targeted biodiversities include deep-sea hot vents of the Arctic mid-ocean ridge (AMOR), the microbiome of the wood-eating Arctic shipworm, thermophilic enrichment cultures from biogas reactors, the Svalbard reindeer gut microbiome, and publicly available metagenomic data from various hot environments. Bioprospecting of the different biodiversities has so far resulted in the discovery of approximately 20 novel enzymes active on lignocellulosic substrates. The significant differences in the origin of the enzymes is reflected in their properties, both beneficial and challenging, and provide us with interesting engineering targets for improved performance in industrial settings. We will present case studies, including work on a novel thermostable cellulase named mgCel6A, with good activity on sulfite-pulped Norway spruce. This enzyme consists of a glycoside hydrolase family 6 catalytic domain (GH6) connected to a family 2 carbohydrate binding module (CBM2) and both the activity profile and predicted structural similarities to known cellulases suggest that mgCel6A is an endo-acting cellulase. Comparison of the full-length enzyme with the catalytic domain showed that the CBM strongly increases substrate binding, while not affecting thermal stability. However, importantly, in reactions with higher substrate concentrations the full-length enzyme was outperformed by the catalytic domain alone, underpinning previous suggestions that CBMs may be less useful in high-consistency bioprocessing. This enzyme is currently being targeted for rational engineering in an effort to decrease the pH optimum and improve the pH stability. Other case studies include GH48 cellulases and lytic polysaccharide monooxygenases (LPMOs). One important aspect of this work concerns the possible assembly of novel enzyme cocktails for lignocellulose processing that can compete with exiting commercial cocktails, which are primarily composed of fungal enzymes. Thus, comparative studies of our most promising bacterial enzymes with their well-known fungal counterparts are also being conducted

Phase diagram of an Ising model with long-range frustrating interactions: a theoretical analysis

We present a theoretical study of the phase diagram of a frustrated Ising model with nearest-neighbor ferromagnetic interactions and long-range (Coulombic) antiferromagnetic interactions. For nonzero frustration, long-range ferromagnetic order is forbidden, and the ground-state of the system consists of phases characterized by periodically modulated structures. At finite temperatures, the phase diagram is calculated within the mean-field approximation. Below the transition line that separates the disordered and the ordered phases, the frustration-temperature phase diagram displays an infinite number of ``flowers'', each flower being made by an infinite number of modulated phases generated by structure combination branching processes. The specificities introduced by the long-range nature of the frustrating interaction and the limitation of the mean-field approach are finally discussed.Comment: 32 pages, 7 figure

Unconventional MBE Strategies from Computer Simulations for Optimized Growth Conditions

We investigate the influence of step edge diffusion (SED) and desorption on Molecular Beam Epitaxy (MBE) using kinetic Monte-Carlo simulations of the solid-on-solid (SOS) model. Based on these investigations we propose two strategies to optimize MBE growth. The strategies are applicable in different growth regimes: During layer-by-layer growth one can exploit the presence of desorption in order to achieve smooth surfaces. By additional short high flux pulses of particles one can increase the growth rate and assist layer-by-layer growth. If, however, mounds are formed (non-layer-by-layer growth) the SED can be used to control size and shape of the three-dimensional structures. By controlled reduction of the flux with time we achieve a fast coarsening together with smooth step edges.Comment: 19 pages, 7 figures, submitted to Phys. Rev.

Large-space shell-model calculations for light nuclei

An effective two-body interaction is constructed from a new Reid-like $NN$ potential for a large no-core space consisting of six major shells and is used to generate the shell-model properties for light nuclei from $A$=2 to 6. (For practical reasons, the model space is partially truncated for $A$=6.) Binding energies and other physical observables are calculated and compare favorably with experiment.Comment: prepared using LaTex, 21 manuscript pages, no figure

Real-time high-resolution mid-infrared optical coherence tomography

The potential for improving the penetration depth of optical coherence tomography systems by using light sources with longer wavelengths has been known since the inception of the technique in the early 1990s. Nevertheless, the development of mid-infrared optical coherence tomography has long been challenged by the maturity and fidelity of optical components in this spectral region, resulting in slow acquisition, low sensitivity, and poor axial resolution. In this work, a mid-infrared spectral-domain optical coherence tomography system operating at a central wavelength of 4?µm and an axial resolution of 8.6?µm is demonstrated. The system produces two-dimensional cross-sectional images in real time enabled by a high-brightness 0.9- to 4.7-µm mid-infrared supercontinuum source with a pulse repetition rate of 1?MHz for illumination and broadband upconversion of more than 1-µm bandwidth from 3.58–4.63?µm to 820–865?nm, where a standard 800-nm spectrometer can be used for fast detection. The images produced by the mid-infrared system are compared with those delivered by a state-of-the-art ultra-high-resolution near-infrared optical coherence tomography system operating at 1.3??m, and the potential applications and samples suited for this technology are discussed. In doing so, the first practical mid-infrared optical coherence tomography system is demonstrated, with immediate applications in real-time non-destructive testing for the inspection of defects and thickness measurements in samples that exhibit strong scattering at shorter wavelengths

Transfer Matrices and Partition-Function Zeros for Antiferromagnetic Potts Models. V. Further Results for the Square-Lattice Chromatic Polynomial

We derive some new structural results for the transfer matrix of square-lattice Potts models with free and cylindrical boundary conditions. In particular, we obtain explicit closed-form expressions for the dominant (at large |q|) diagonal entry in the transfer matrix, for arbitrary widths m, as the solution of a special one-dimensional polymer model. We also obtain the large-q expansion of the bulk and surface (resp. corner) free energies for the zero-temperature antiferromagnet (= chromatic polynomial) through order q^{-47} (resp. q^{-46}). Finally, we compute chromatic roots for strips of widths 9 <= m <= 12 with free boundary conditions and locate roughly the limiting curves.Comment: 111 pages (LaTeX2e). Includes tex file, three sty files, and 19 Postscript figures. Also included are Mathematica files data_CYL.m and data_FREE.m. Many changes from version 1: new material on series expansions and their analysis, and several proofs of previously conjectured results. Final version to be published in J. Stat. Phy

A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011