Dynamical Properties of a Growing Surface on a Random Substrate

The dynamics of the discrete Gaussian model for the surface of a crystal deposited on a disordered substrate is investigated by Monte Carlo simulations. The mobility of the growing surface was studied as a function of a small driving force $F$ and temperature $T$. A continuous transition is found from high-temperature phase characterized by linear response to a low-temperature phase with nonlinear, temperature dependent response. In the simulated regime of driving force the numerical results are in general agreement with recent dynamic renormalization group predictions.Comment: 10 pages, latex, 3 figures, to appear in Phys. Rev. E (RC

Large‑scale analysis of iliopsoas muscle volumes in the UK Biobank

Psoas muscle measurements are frequently used as markers of sarcopenia and predictors of health. Manually measured cross-sectional areas are most commonly used, but there is a lack of consistency regarding the position of the measurement and manual annotations are not practical for large population studies. We have developed a fully automated method to measure iliopsoas muscle volume (comprised of the psoas and iliacus muscles) using a convolutional neural network. Magnetic resonance images were obtained from the UK Biobank for 5000 participants, balanced for age, gender and BMI. Ninety manual annotations were available for model training and validation. The model showed excellent performance against out-of-sample data (average dice score coefficient of 0.9046 ± 0.0058 for six-fold cross-validation). Iliopsoas muscle volumes were successfully measured in all 5000 participants. Iliopsoas volume was greater in male compared with female subjects. There was a small but significant asymmetry between left and right iliopsoas muscle volumes. We also found that iliopsoas volume was significantly related to height, BMI and age, and that there was an acceleration in muscle volume decrease in men with age. Our method provides a robust technique for measuring iliopsoas muscle volume that can be applied to large cohorts

Crystal surfaces with correlated disorder: Phase transitions between roughening and superroughening

A theory for surface transitions in the presence of a disordered pinning potential is presented. Arbitrary disorder correlations are treated in the framework of a dynamical functional renormalization group. The roughening transition, where surface roughness and mobility behave discontinuously, is shown to turn smoothly into the continuous superroughening transition, when the range of disorder correlations is decreased. Implications for random-field $XY$-models and vortex glasses are discussed.Comment: 13 pages with 2 figures, latex+revte

ABC-SysBio-approximate Bayesian computation in Python with GPU support.

Motivation: The growing field of systems biology has driven demand for flexible tools to model and simulate biological systems. Two established problems in the modeling of biological processes are model selection and the estimation of associated parameters. A number of statistical approaches, both frequentist and Bayesian, have been proposed to answer these questions. Results: Here we present a Python package, ABC-SysBio, that implements parameter inference and model selection for dynamical systems in an approximate Bayesian computation (ABC) framework. ABC-SysBio combines three algorithms: ABC rejection sampler, ABC SMC for parameter inference and ABC SMC for model selection. It is designed to work with models written in Systems Biology Markup Language (SBML). Deterministic and stochastic models can be analyzed in ABC-SysBio

Force fluctuation in a driven elastic chain

We study the dynamics of an elastic chain driven on a disordered substrate and analyze numerically the statistics of force fluctuations at the depinning transition. The probability distribution function of the amplitude of the slip events for small velocities is a power law with an exponent $+AFw-tau$ depending on the driving velocity. This result is in qualitative agreement with experimental measurements performed on sliding elastic surfaces with macroscopic asperities. We explore the properties of the depinning transition as a function of the driving mode (i.e. constant force or constant velocity) and compute the force-velocity diagram using finite size scaling methods. The scaling exponents are in excellent agreement with the values expected in interface models and, contrary to previous studies, we found no difference in the exponents for periodic and disordered chains.Comment: 8 page

New evidence for super-roughening in crystalline surfaces with disordered substrate

We study the behavior of the Binder cumulant related to long distance correlation functions of the discrete Gaussian model of disordered substrate crystalline surfaces. We exhibit numerical evidence that the non-Gaussian behavior in the low-$T$ region persists on large length scales, in agreement with the broken phase being super-rough.Comment: 10 pages and 4 figures, available at http://chimera.roma1.infn.it/index_papers_complex.html . We have extended the RG discussion and minor changes in the tex

Ground-State Roughness of the Disordered Substrate and Flux Line in d=2

We apply optimization algorithms to the problem of finding ground states for crystalline surfaces and flux lines arrays in presence of disorder. The algorithms provide ground states in polynomial time, which provides for a more precise study of the interface widths than from Monte Carlo simulations at finite temperature. Using $d=2$ systems up to size $420^2$, with a minimum of $2 \times 10^3$ realizations at each size, we find very strong evidence for a $\ln^2(L)$ super-rough state at low temperatures.Comment: 10 pages, 3 PS figures, to appear in PR

Ground state properties of solid-on-solid models with disordered substrates

We study the glassy super-rough phase of a class of solid-on-solid models with a disordered substrate in the limit of vanishing temperature by means of exact ground states, which we determine with a newly developed minimum cost flow algorithm. Results for the height-height correlation function are compared with analytical and numerical predictions. The domain wall energy of a boundary induced step grows logarithmically with system size, indicating the marginal stability of the ground state, and the fractal dimension of the step is estimated. The sensibility of the ground state with respect to infinitesimal variations of the quenched disorder is analyzed.Comment: 4 pages RevTeX, 3 eps-figures include

Static and Dynamic Properties of Inhomogeneous Elastic Media on Disordered Substrate

The pinning of an inhomogeneous elastic medium by a disordered substrate is studied analytically and numerically. The static and dynamic properties of a $D$-dimensional system are shown to be equivalent to those of the well known problem of a $D$-dimensional random manifold embedded in $(D+D)$-dimensions. The analogy is found to be very robust, applicable to a wide range of elastic media, including those which are amorphous or nearly-periodic, with local or nonlocal elasticity. Also demonstrated explicitly is the equivalence between the dynamic depinning transition obtained at a constant driving force, and the self-organized, near-critical behavior obtained by a (small) constant velocity drive.Comment: 20 pages, RevTeX. Related (p)reprints also available at http://matisse.ucsd.edu/~hwa/pub.htm

Interacting Arrays of Steps and Lines in Random Media

The phase diagram of two interacting planar arrays of directed lines in random media is obtained by a renormalization group analysis. The results are discussed in the contexts of the roughening of reconstructed crystal surfaces, and the pinning of flux line arrays in layered superconductors. Among the findings are a glassy flat phase with disordered domain structures, a novel second-order phase transition with continuously varying critical exponents, and the generic disappearance of the glassy ``super-rough'' phases found previously for a single array.Comment: 4 pages, REVTEX 3.0, uses epsf,multicol, 3 .eps-figures, submitted to PR