Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.Comment: 8 pages, 6 figure

A reduced model for shock and detonation waves. II. The reactive case

We present a mesoscopic model for reactive shock waves, which extends a previous model proposed in [G. Stoltz, Europhys. Lett. 76 (2006), 849]. A complex molecule (or a group of molecules) is replaced by a single mesoparticle, evolving according to some Dissipative Particle Dynamics. Chemical reactions can be handled in a mean way by considering an additional variable per particle describing a rate of reaction. The evolution of this rate is governed by the kinetics of a reversible exothermic reaction. Numerical results give profiles in qualitative agreement with all-atom studies

Lignin dynamics in two13C-labelled arable soils during 18 years

Lignin has long been considered a relatively stable component of soil organic matter. However, recent studies suggest that lignin may turn over within years to decades in arable soil. Here we analyzed lignin concentrations in an 18 year field experiment under continuous silage maize where two soils were sampled at six points in time. Our objectives were to examine the long-term dynamics of (i) lignin derived from a previous C3-vegetation and (ii) lignin derived from maize, as influenced by two levels of maize biomass input. Total lignin concentrations in soil were quantified by gas chromatography of lignin cupric oxide oxidation products. Compound-specific 13C isotope analysis allowed discrimination between C3-derived lignin and maize-derived lignin. Degradation dynamics of C3-derived lignin were independent of biomass input level, suggesting that priming did not affect soil lignin concentrations over almost two decades. After 18 years approximately two thirds of the initial C3-derived lignin remained in the soils, whereas, on average, 10 % of the recent maize-derived lignin input was retained. We suggest that lignin is effectively stabilized in these arable soils, although the mechanisms involved remain unclear

Dynamics of the Pionium with the Density Matrix Formalism

The evolution of pionium, the $\pi^+ \pi^-$ hydrogen-like atom, while passing through matter is solved within the density matrix formalism in the first Born approximation. We compare the influence on the pionium break-up probability between the standard probabilistic calculations and the more precise picture of the density matrix formalism accounting for interference effects. We focus our general result in the particular conditions of the DIRAC experiment at CERN.Comment: 14 pages, 2 figures, submitted to J. Phys. B: At. Mol. Phy

Development of a Forced Oscillation System for Measuring Dynamic Derivatives of Fluidic Vehicles

A new Forced Oscillation System (FOS) has been designed and built at NASA Langley Research Center that provides new capabilities for aerodynamic researchers to investigate the dynamic derivatives of vehicle configurations. Test vehicles may include high performance and general aviation aircraft, re-entry spacecraft, submarines and other fluidic vehicles. The measured data from forced oscillation testing is used in damping characteristic studies and in simulation databases for control algorithm development and performance analyses. The newly developed FOS hardware provides new flexibility for conducting dynamic derivative studies. The design is based on a tracking principle where a desired motion profile is achieved via a fast closed-loop positional controller. The motion profile for the tracking system is numerically generated and thus not limited to sinusoidal motion. This approach permits non-traditional profiles such as constant velocity and Schroeder sweeps. Also, the new system permits changes in profile parameters including nominal offset angle, waveform, and associated parameters such as amplitude and frequency. Most importantly, the changes may be made remotely without halting the FOS and the tunnel. System requirements, system analysis, and the resulting design are addressed for a new FOS in the 12-Foot Low-Speed Wind Tunnel (LSWT). The overall system including mechanical, electrical, and control subsystems is described. The design is complete, and the FOS has been built and installed in the 12-Foot LSWT. System integration and testing have verified design intent and safe operation. Currently it is being validated for wind-tunnel operations and aerodynamic testing. The system is a potential major enhancement to forced oscillation studies. The productivity gain from the motion profile automation will shorten the testing cycles needed for control surface and aircraft control algorithm development. The new motion capabilities also will serve as a test bed for researchers to study and to improve and/or alter future forced oscillation testing techniques

The extreme mobility of debris avalanches: A new model of transport mechanism

International audienceLarge rockslide-debris avalanches, resulting from flank collapses that shape volcanoes and mountains on Earth and other object of the solar system, are rapid and dangerous gravity-driven granular flows that travel abnormal distances. During the last 50 years, numerous physical models have been put forward to explain their extreme mobility. The principal models are based on fluidization, lubrication, or dynamic disintegration. However, these processes remain poorly constrained. To identify precisely the transport mechanisms during debris avalanches, we examined morphometric (fractal dimension and circularity), grain size, and exoscopic characteristics of the various types of particles (clasts and matrix) from volcanic debris avalanche deposits of La Réunion Island (Indian Ocean). From these data we demonstrate for the first time that syn-transport dynamic disintegration continuously operates with the increasing runout distance from the source down to a grinding limit of 500 μm. Below this limit, the particle size reduction exclusively results from their attrition by frictional interactions. Consequently, the exceptional mobility of debris avalanches may be explained by the combined effect of elastic energy release during the dynamic disintegration of the larger clasts and frictional reduction within the matrix due to interactions between the finer particles

Coherent and incoherent atomic scattering: Formalism and application to pionium interacting with matter

The experimental determination of the lifetime of pionium provides a very important test on chiral perturbation theory. This quantity is determined in the DIRAC experiment at CERN. In the analysis of this experiment, the breakup probabilities of of pionium in matter are needed to high accuracy as a theoretical input. We study in detail the influence of the target electrons. They contribute through screening and incoherent effects. We use Dirac-Hartree- Fock-Slater wavefunctions in order to determine the corresponding form factors. We find that the inner-shell electrons contribute less than the weakly bound outer electrons. Furthermore, we establish a more rigorous estimate for the magnitude of the contributions form the transverse current (magnetic terms thus far neglected in the calculations).Comment: Journal of Physics B: Atomic, Molecular and Optical Physics; (accepted; 22 pages, 6 figures, 26 references) Revised version: more detailed description of DIRAC experiment; failure of simplest models for incoherent scattering demonstrated by example

Theory of Bi2_2Sr2_2CaCu2_2O8+δ_{8+\delta} Cross-Whisker Josephson Junctions

Takano {\it et al.} [Phys. Rev. B {\bf 65}, 140513 (2002) and unpublished] made Josephson junctions from single crystal whiskers of Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ crossed an angle $\phi_0$ about the $c$ axis. From the mesa structures that formed at the cross-whisker interface, they inferred a critical current density $J_c(\phi_0)$. Like the single crystal results of Li {\it et al.} [Phys. Rev. Lett. {\bf 83}, 4160 (1999)], we show that the whisker data are unlikely to result from a predominantly d-wave order parameter. However, unlike the single crystals, these results, if correct, require the whisker c-axis transport to be coherent.Comment: 5 pages, 4 figures, accepted for publication in Physical Review

Pattern formation during the evaporation of a colloidal nanoliter drop: a numerical and experimental study

An efficient way to precisely pattern particles on solid surfaces is to dispense and evaporate colloidal drops, as for bioassays. The dried deposits often exhibit complex structures exemplified by the coffee ring pattern, where most particles have accumulated at the periphery of the deposit. In this work, the formation of deposits during the drying of nanoliter colloidal drops on a flat substrate is investigated numerically and experimentally. A finite-element numerical model is developed that solves the Navier-Stokes, heat and mass transport equations in a Lagrangian framework. The diffusion of vapor in the atmosphere is solved numerically, providing an exact boundary condition for the evaporative flux at the droplet-air interface. Laplace stresses and thermal Marangoni stresses are accounted for. The particle concentration is tracked by solving a continuum advection-diffusion equation. Wetting line motion and the interaction of the free surface of the drop with the growing deposit are modeled based on criteria on wetting angles. Numerical results for evaporation times and flow field are in very good agreement with published experimental and theoretical results. We also performed transient visualization experiments of water and isopropanol drops loaded with polystyrene microsphere evaporating on respectively glass and polydimethylsiloxane substrates. Measured evaporation times, deposit shape and sizes, and flow fields are in very good agreement with the numerical results. Different flow patterns caused by the competition of Marangoni loops and radial flow are shown to determine the deposit shape to be either a ring-like pattern or a homogeneous bump