Critical free energy and Casimir forces in rectangular geometries

We study the critical behavior of the free energy and the thermodynamic Casimir force in a $L_\parallel^{d-1} \times L$ block geometry in $2<d<4$ dimensions with aspect ratio $\rho=L/L_\parallel$ above, at, and below $T_c$ on the basis of the O$(n)$ symmetric $\phi^4$ lattice model with periodic boundary conditions (b.c.). We consider a simple-cubic lattice with isotropic short-range interactions. Exact results are derived in the large - $n$ limit describing the geometric crossover from film ($\rho =0$) over cubic $\rho=1$ to cylindrical ($\rho = \infty$) geometries. For $n=1$, three perturbation approaches are presented that cover both the central finite-size regime near $T_c$ for $1/4 \lesssim \rho \lesssim 3$ and the region outside the central finite-size regime well above and below $T_c$ for arbitrary $\rho$. At bulk $T_c$ of isotropic systems with periodic b.c., we predict the critical Casimir force in the vertical $(L)$ direction to be negative (attractive) for a slab ($\rho 1$), and zero for a cube $(\rho=1)$. We also present extrapolations to the cylinder limit ($\rho=\infty$) and to the film limit ($\rho=0$) for $n=1$ and $d=3$. Our analytic results for finite-size scaling functions in the minimal renormalization scheme at fixed dimension $d=3$ agree well with Monte Carlo data for the three-dimensional Ising model by Hasenbusch for $\rho=1$ and by Vasilyev et al. for $\rho=1/6$ above, at, and below $T_c$.Comment: 23 pages, 14 figure

Scaling of thermal conductivity of helium confined in pores

We have studied the thermal conductivity of confined superfluids on a bar-like geometry. We use the planar magnet lattice model on a lattice $H\times H\times L$ with $L \gg H$. We have applied open boundary conditions on the bar sides (the confined directions of length $H$) and periodic along the long direction. We have adopted a hybrid Monte Carlo algorithm to efficiently deal with the critical slowing down and in order to solve the dynamical equations of motion we use a discretization technique which introduces errors only $O((\delta t)^6)$ in the time step $\delta t$. Our results demonstrate the validity of scaling using known values of the critical exponents and we obtained the scaling function of the thermal resistivity. We find that our results for the thermal resistivity scaling function are in very good agreement with the available experimental results for pores using the tempComment: 5 two-column pages, 3 figures, Revtex

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

ABSTRACT: BACKGROUND: The generation and analysis of high-throughput sequencing data are becoming a major component of many studies in molecular biology and medical research. Illumina's Genome Analyzer (GA) and HiSeq instruments are currently the most widely used sequencing devices. Here, we comprehensively evaluate properties of genomic HiSeq and GAIIx data derived from two plant genomes and one virus, with read lengths of 95 to 150 bases. RESULTS: We provide quantifications and evidence for GC bias, error rates, error sequence context, effects of quality filtering, and the reliability of quality values. By combining different filtering criteria we reduced error rates 7-fold at the expense of discarding 12.5% of alignable bases. While overall error rates are low in HiSeq data we observed regions of accumulated wrong base calls. Only 3% of all error positions accounted for 24.7% of all substitution errors. Analyzing the forward and reverse strands separately revealed error rates of up to 18.7%. Insertions and deletions occurred at very low rates on average but increased to up to 2% in homopolymers. A positive correlation between read coverage and GC content was found depending on the GC content range. CONCLUSIONS: The errors and biases we report have implications for the use and the interpretation of Illumina sequencing data. GAIIx and HiSeq data sets show slightly different error profiles. Quality filtering is essential to minimize downstream analysis artifacts. Supporting previous recommendations, the strand-specificity provides a criterion to distinguish sequencing errors from low abundance polymorphisms

Critical Behavior of O(n)-symmetric Systems With Reversible Mode-coupling Terms: Stability Against Detailed-balance Violation

We investigate nonequilibrium critical properties of $O(n)$-symmetric models with reversible mode-coupling terms. Specifically, a variant of the model of Sasv\'ari, Schwabl, and Sz\'epfalusy is studied, where violation of detailed balance is incorporated by allowing the order parameter and the dynamically coupled conserved quantities to be governed by heat baths of different temperatures $T_S$ and $T_M$, respectively. Dynamic perturbation theory and the field-theoretic renormalization group are applied to one-loop order, and yield two new fixed points in addition to the equilibrium ones. The first one corresponds to $\Theta = T_S / T_M = \infty$ and leads to model A critical behavior for the order parameter and to anomalous noise correlations for the generalized angular momenta; the second one is at $\Theta = 0$ and is characterized by mean-field behavior of the conserved quantities, by a dynamic exponent $z = d / 2$ equal to that of the equilibrium SSS model, and by modified static critical exponents. However, both these new fixed points are unstable, and upon approaching the critical point detailed balance is restored, and the equilibrium static and dynamic critical properties are recovered.Comment: 18 pages, RevTeX, 1 figure included as eps-file; submitted to Phys. Rev.

Thinning of superfluid films below the critical point

Experiments on $^4$He films reveal an attractive Casimir-like force at the bulk $\lambda$-point, and in the superfluid regime. Previous work has explained the magnitude of this force at the $\lambda$ transition and deep in the superfluid region but not the substantial attractive force immediately below the $\lambda$-point. Utilizing a simple mean-field calculation renormalized by critical fluctuations we obtain an effective Casimir force that is qualitatively consistent with the scaling function $\vartheta$ obtained by collapse of experimental data.Comment: 4 page

Non-universal size dependence of the free energy of confined systems near criticality

The singular part of the finite-size free energy density $f_s$ of the O(n) symmetric $\phi^4$ field theory in the large-n limit is calculated at finite cutoff for confined geometries of linear size L with periodic boundary conditions in 2 < d < 4 dimensions. We find that a sharp cutoff $\Lambda$ causes a non-universal leading size dependence $f_s \sim \Lambda^{d-2} L^{-2}$ near $T_c$ which dominates the universal scaling term $\sim L^{-d}$. This implies a non-universal critical Casimir effect at $T_c$ and a leading non-scaling term $\sim L^{-2}$ of the finite-size specific heat above $T_c$.Comment: RevTex, 4 page