Effective thermodynamics of strongly coupled qubits

Interactions between a quantum system and its environment at low temperatures can lead to violations of thermal laws for the system. The source of these violations is the entanglement between system and environment, which prevents the system from entering into a thermal state. On the other hand, for two-state systems, we show that one can define an effective temperature, placing the system into a `pseudo-thermal' state where effective thermal laws are upheld. We then numerically explore these assertions for an n-state system inspired by the spin-boson environment.Comment: 9 pages, 3 figure

Stripe-hexagon competition in forced pattern forming systems with broken up-down symmetry

We investigate the response of two-dimensional pattern forming systems with a broken up-down symmetry, such as chemical reactions, to spatially resonant forcing and propose related experiments. The nonlinear behavior immediately above threshold is analyzed in terms of amplitude equations suggested for a $1:2$ and $1:1$ ratio between the wavelength of the spatial periodic forcing and the wavelength of the pattern of the respective system. Both sets of coupled amplitude equations are derived by a perturbative method from the Lengyel-Epstein model describing a chemical reaction showing Turing patterns, which gives us the opportunity to relate the generic response scenarios to a specific pattern forming system. The nonlinear competition between stripe patterns and distorted hexagons is explored and their range of existence, stability and coexistence is determined. Whereas without modulations hexagonal patterns are always preferred near onset of pattern formation, single mode solutions (stripes) are favored close to threshold for modulation amplitudes beyond some critical value. Hence distorted hexagons only occur in a finite range of the control parameter and their interval of existence shrinks to zero with increasing values of the modulation amplitude. Furthermore depending on the modulation amplitude the transition between stripes and distorted hexagons is either sub- or supercritical.Comment: 10 pages, 12 figures, submitted to Physical Review

A novel, fast, HMM-with-Duration implementation – for application with a new, pattern recognition informed, nanopore detector

<p>Abstract</p> <p>Background</p> <p>Hidden Markov Models (HMMs) provide an excellent means for structure identification and feature extraction on stochastic sequential data. An HMM-with-Duration (HMMwD) is an HMM that can also exactly model the hidden-label length (recurrence) distributions – while the regular HMM will impose a best-fit geometric distribution in its modeling/representation.</p> <p>Results</p> <p>A Novel, Fast, HMM-with-Duration (HMMwD) Implementation is presented, and experimental results are shown that demonstrate its performance on two-state synthetic data designed to model Nanopore Detector Data. The HMMwD experimental results are compared to (i) the ideal model and to (ii) the conventional HMM. Its accuracy is clearly an improvement over the standard HMM, and matches that of the ideal solution in many cases where the standard HMM does not. Computationally, the new HMMwD has all the speed advantages of the conventional (simpler) HMM implementation. In preliminary work shown here, HMM feature extraction is then used to establish the first pattern recognition-informed (PRI) sampling control of a Nanopore Detector Device (on a "live" data-stream).</p> <p>Conclusion</p> <p>The improved accuracy of the new HMMwD implementation, at the same order of computational cost as the standard HMM, is an important augmentation for applications in gene structure identification and channel current analysis, especially PRI sampling control, for example, where speed is essential. The PRI experiment was designed to inherit the high accuracy of the well characterized and distinctive blockades of the DNA hairpin molecules used as controls (or blockade "test-probes"). For this test set, the accuracy inherited is 99.9%.</p

Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions

<p>Abstract</p> <p>Background</p> <p>The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector.</p> <p>Results</p> <p>We present evidence that different forms of channel blockade can be associated with the same antibody, we associate these different blockades with different orientations of "capture" of an antibody in the detector's nanometer-scale channel. We directly detect the presence of antibodies via reductions in channel current. Changes to blockade patterns upon addition of antigen suggest indirect detection of antibody/antigen binding. Similarly, DNA-hairpin anchored antibodies have been studied, where the DNA linkage is to the carboxy-terminus at the base of the antibody's Fc region, with significantly fewer types of (lengthy) capture blockades than was observed for free (un-bound) IgG antibody. The introduction of chaotropic agents and its effects on protein-protein interactions have also been observed.</p> <p>Conclusion</p> <p>Nanopore-based approaches may eventually provide a direct analysis of the complex conformational "negotiations" that occur upon binding between proteins.</p

Dynamic response of berea sandstone shock-loaded under dry, wet and water-pressurized conditions

A single-stage light-gas gun was used to perform shock-recovery experiments on Berea sandstone under dry, wet and hydrostatically water-pressurized conditions. The samples were impacted by flyer-plates to achieve stress levels in the range 1.3 to 9.8 GPa. The microstructure of the shocked samples was analyzed using scanning electron microscopy (SEM), laser particle analysis and X-ray computed microtomography (XCMT). The dry samples show strongly fragmented and irregularly fractured quartz grains with a considerably reduced porosity, whereas the wet and water-pressurized specimens show less grain damage and less porosity reduction. During shock compression the water in the pores distributes the stresses and therefore the contact force between the grains is reduced. The interaction between the grains during the shock process was modeled by explicitly treating the grain-pore structure using Smooth Particle Hydrodynamics (SPH) and the Discrete Element Method (DEM)

Convection in colloidal suspensions with particle-concentration-dependent viscosity

The onset of thermal convection in a horizontal layer of a colloidal suspension is investigated in terms of a continuum model for binary-fluid mixtures where the viscosity depends on the local concentration of colloidal particles. With an increasing difference between the viscosity at the warmer and the colder boundary the threshold of convection is reduced in the range of positive values of the separation ratio psi with the onset of stationary convection as well as in the range of negative values of psi with an oscillatory Hopf bifurcation. Additionally the convection rolls are shifted downwards with respect to the center of the horizontal layer for stationary convection (psi>0) and upwards for the Hopf bifurcation (psi<0).Comment: 8 pages, 6 figures, submitted to European Physical Journal

Localized and Delocalized Charge Transport in Single-Wall Carbon-Nanotube Mats

We measured the complex dielectric constant in mats of single-wall carbon-nanotubes between 2.7 K and 300 K up to 0.5 THz. The data are well understood in a Drude approach with a negligible temperature dependence of the plasma frequency (omega_p) and scattering time (tau) with an additional contribution of localized charges. The dielectric properties resemble those of the best ''metallic'' polypyrroles and polyanilines. The absence of metallic islands makes the mats a relevant piece in the puzzle of the interpretation of tau and omega_p in these polymers.Comment: 4 pages including 4 figure