Ground state properties of fluxlines in a disordered environment

A new numerical method to calculate exact ground states of multi-fluxline systems with quenched disorder is presented, which is based on the minimum cost flow algorithm from combinatorial optimization. We discuss several models that can be studied with this method including their specific implementations, physically relevant observables and results: 1) the N-line model with N fluxlines (or directed polymers) in a d-dimensional environment with point and/or columnar disorder and hard or soft core repulsion; 2) the vortex glass model for a disordered superconductor in the strong screening limit and 3) the Sine-Gordon model with random pase shifts in the strong coupling limit.Comment: 4 pages RevTeX, 3 eps-figures include

Application of a minimum cost flow algorithm to the three-dimensional gauge glass model with screening

We study the three-dimensional gauge glass model in the limit of strong screening by using a minimum cost flow algorithm, enabling us to obtain EXACT ground states for systems of linear size L<=48. By calculating the domain-wall energy, we obtain the stiffness exponent theta = -0.95+/-0.03, indicating the absence of a finite temperature phase transition, and the thermal exponent nu=1.05+/-0.03. We discuss the sensitivity of the ground state with respect to small perturbations of the disorder and determine the overlap length, which is characterized by the chaos exponent zeta=3.9+/-0.2, implying strong chaos.Comment: 4 pages RevTeX, 2 eps-figures include

Superconductor-to-Normal Phase Transition in a Vortex Glass Model: Numerical Evidence for a New Percolation Universality Class

The three-dimensional strongly screened vortex-glass model is studied numerically using methods from combinatorial optimization. We focus on the effect of disorder strength on the ground state and found the existence of a disorder-driven normal-to-superconducting phase transition. The transition turns out to be a geometrical phase transition with percolating vortex loops in the ground state configuration. We determine the critical exponents and provide evidence for a new universality class of correlated percolation.Comment: 11 pages LaTeX using IOPART.cls, 11 eps-figures include

Numerical Study of Order in a Gauge Glass Model

The XY model with quenched random phase shifts is studied by a T=0 finite size defect energy scaling method in 2d and 3d. The defect energy is defined by a change in the boundary conditions from those compatible with the true ground state configuration for a given realization of disorder. A numerical technique, which is exact in principle, is used to evaluate this energy and to estimate the stiffness exponent $\theta$. This method gives $\theta = -0.36\pm0.013$ in 2d and $\theta = +0.31\pm 0.015$ in 3d, which are considerably larger than previous estimates, strongly suggesting that the lower critical dimension is less than three. Some arguments in favor of these new estimates are given.Comment: 4 pages, 2 figures, revtex. Submitted to Phys. Rev. Let

A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low

Efficient Reverse Transcription Using Locked Nucleic Acid Nucleotides towards the Evolution of Nuclease Resistant RNA Aptamers

Background: Modified nucleotides are increasingly being utilized in the de novo selection of aptamers for enhancing their drug-like character and abolishing the need for time consuming trial-and-error based post-selection modifications. Locked nucleic acid (LNA) is one of the most prominent and successful nucleic acid analogues because of its remarkable properties, and widely explored as building blocks in therapeutic oligonucleotides. Evolution of LNA-modified RNA aptamers requires an efficient reverse transcription method for PCR enrichment of the selected RNA aptamer candidates. Establishing this key step is a pre-requisite for performing LNA-modified RNA aptamer selection

Investigation of growth responses in saprophytic fungi to charred biomass

We present the results of a study testing the response of two saprophytic white-rot fungi species, Pleurotus pulmonarius and Coriolus versicolor, to charred biomass (charcoal) as a growth substrate. We used a combination of optical microscopy, scanning electron microscopy, elemental abundance measurements, and isotope ratio mass spectrometry (&lt;sup&gt;13&lt;/sup&gt;C and &lt;sup&gt;15&lt;/sup&gt;N) to investigate fungal colonisation of control and incubated samples of Scots Pine (Pinus sylvestris) wood, and charcoal from the same species produced at 300 °C and 400 °C. Both species of fungi colonise the surface and interior of wood and charcoals over time periods of less than 70 days; however, distinctly different growth forms are evident between the exterior and interior of the charcoal substrate, with hyphal penetration concentrated along lines of structural weakness. Although the fungi were able to degrade and metabolise the pine wood, charcoal does not form a readily available source of fungal nutrients at least for these species under the conditions used in this study

Current-voltage scaling of chiral and gauge-glass models of two-dimensional superconductors

The scaling behavior of the current-voltage characteristics of chiral and gauge glass models of disordered superconductors, are studied numerically, in two dimensions. For both models, the linear resistance is nonzero at finite temperatures and the scaling analysis of the nonlinear resistivity is consistent with a phase transition at T=0 temperature characterized by a diverging correlation length $\xi \propto T^{-\nu_{T}}$ and thermal critical exponent $\nu_{T}$. The values of $\nu_{T}$, however, are found to be different for the chiral and gauge glass models, suggesting different universality classes, in contrast to the result obtained recently in three dimensions.Comment: 4 pages, 4 figures (included), to appear in Phys. Rev.

Defect-unbinding and the Bose-glass transition in layered superconductors

The low-field Bose-glass transition temperature in heavy-ion irradiated Bi_2Sr_2CaCu_2O_8+d increases progressively with increasing density of irradiation-induced columnar defects, but saturates for densities in excess of 1.5 x10^9 cm^-2. The maximum Bose-glass temperature corresponds to that above which diffusion of two-dimensional pancake vortices between different vortex lines becomes possible, and above which the ``line-like'' character of vortices is lost. We develop a description of the Bose-glass line that is in excellent quantitative agreement with the experimental line obtained for widely different values of track density and material parameters.Comment: 4 pages, 4 figures, submitted to Phys. Rev. Let

Long Range Order at Low Temperature in Dipolar Spin Ice

Recently it has been suggested that long range magnetic dipolar interactions are responsible for spin ice behavior in the Ising pyrochlore magnets ${\rm Dy_{2}Ti_{2}O_{7}}$ and ${\rm Ho_{2}Ti_{2}O_{7}}$. We report here numerical results on the low temperature properties of the dipolar spin ice model, obtained via a new loop algorithm which greatly improves the dynamics at low temperature. We recover the previously reported missing entropy in this model, and find a first order transition to a long range ordered phase with zero total magnetization at very low temperature. We discuss the relevance of these results to ${\rm Dy_{2}Ti_{2}O_{7}}$ and ${\rm Ho_{2}Ti_{2}O_{7}}$.Comment: New version of the manuscript. Now contains 3 POSTSCRIPT figures as opposed to 2 figures. Manuscript contains a more detailed discussion of the (i) nature of long-range ordered ground state, (ii) finite-size scaling results of the 1st order transition into the ground state. Order of authors has been changed. Resubmitted to Physical Review Letters Contact: [email protected]