Measurement of Lagrangian velocity in fully developed turbulence

We have developed a new experimental technique to measure the Lagrangian velocity of tracer particles in a turbulent flow, based on ultrasonic Doppler tracking. This method yields a direct access to the velocity of a single particule at a turbulent Reynolds number $R_{\lambda} = 740$. Its dynamics is analyzed with two decades of time resolution, below the Lagrangian correlation time. We observe that the Lagrangian velocity spectrum has a Lorentzian form $E^{L}(\omega) = u_{rms}^{2} T_{L} / (1 + (T_{L}\omega)^{2})$, in agreement with a Kolmogorov-like scaling in the inertial range. The probability density function (PDF) of the velocity time increments displays a change of shape from quasi-Gaussian a integral time scale to stretched exponential tails at the smallest time increments. This intermittency, when measured from relative scaling exponents of structure functions, is more pronounced than in the Eulerian framework.Comment: 4 pages, 5 figures. to appear in PR

Precision Measurements of Stretching and Compression in Fluid Mixing

The mixing of an impurity into a flowing fluid is an important process in many areas of science, including geophysical processes, chemical reactors, and microfluidic devices. In some cases, for example periodic flows, the concepts of nonlinear dynamics provide a deep theoretical basis for understanding mixing. Unfortunately, the building blocks of this theory, i.e. the fixed points and invariant manifolds of the associated Poincare map, have remained inaccessible to direct experimental study, thus limiting the insight that could be obtained. Using precision measurements of tracer particle trajectories in a two-dimensional fluid flow producing chaotic mixing, we directly measure the time-dependent stretching and compression fields. These quantities, previously available only numerically, attain local maxima along lines coinciding with the stable and unstable manifolds, thus revealing the dynamical structures that control mixing. Contours or level sets of a passive impurity field are found to be aligned parallel to the lines of large compression (unstable manifolds) at each instant. This connection appears to persist as the onset of turbulence is approached.Comment: 5 pages, 5 figure

Semiclassical time evolution of the density matrix and tunneling

The time dependent density matrix of a system with potential barrier is studied using path integrals. The characterization of the initial state, which is assumed to be restricted to one side of the barrier, and the time evolution of the density matrix lead to a three-fold path integral which is evaluated in the semiclassical limit. The semiclassical trajectories are found to move in the complex coordinate plane and barrier penetration only arises due to fluctuations. Both the form of the semiclassical paths and the relevant fluctuations change significantly as a function of temperature. The semiclassical analysis leads to a detailed picture of barrier penetration in the real time domain and the changeover from thermal activation to quantum tunneling. Deep tunneling is associated with quasi-zero modes in the fluctuation spectrum about the semiclassical orbits in the long time limit. The connection between this real time description of tunneling and the standard imaginary time instanton approach is established. Specific results are given for a double well potential and an Eckart barrier.Comment: 27 pages, 8 figures, to be published in Phys. Rev.

Floquet-Markov description of the parametrically driven, dissipative harmonic quantum oscillator

Using the parametrically driven harmonic oscillator as a working example, we study two different Markovian approaches to the quantum dynamics of a periodically driven system with dissipation. In the simpler approach, the driving enters the master equation for the reduced density operator only in the Hamiltonian term. An improved master equation is achieved by treating the entire driven system within the Floquet formalism and coupling it to the reservoir as a whole. The different ensuing evolution equations are compared in various representations, particularly as Fokker-Planck equations for the Wigner function. On all levels of approximation, these evolution equations retain the periodicity of the driving, so that their solutions have Floquet form and represent eigenfunctions of a non-unitary propagator over a single period of the driving. We discuss asymptotic states in the long-time limit as well as the conservative and the high-temperature limits. Numerical results obtained within the different Markov approximations are compared with the exact path-integral solution. The application of the improved Floquet-Markov scheme becomes increasingly important when considering stronger driving and lower temperatures.Comment: 29 pages, 7 figure

Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores.

Clostridium difficile is the leading cause of hospital acquired diarrhoea in industrialised countries. Under conditions that are not favourable for growth, the pathogen produces metabolically dormant endospores via asymmetric cell division. These are extremely resistant to both chemical and physical stress and provide the mechanism by which C. difficile can evade the potentially fatal consequences of exposure to heat, oxygen, alcohol, and certain disinfectants. Spores are the primary infective agent and must germinate to allow for vegetative cell growth and toxin production. While spore germination in Bacillus is well understood, little is known about C. difficile germination and outgrowth. Here we use genome-wide transcriptional analysis to elucidate the temporal gene expression patterns in C. difficile 630 endospore germination. We have optimized methods for large scale production and purification of spores. The germination characteristics of purified spores have been characterized and RNA extraction protocols have been optimized. Gene expression was highly dynamic during germination and outgrowth, and was found to involve a large number of genes. Using this genome-wide, microarray approach we have identified 511 genes that are significantly up- or down-regulated during C. difficile germination (p≤0.01). A number of functional groups of genes appeared to be co-regulated. These included transport, protein synthesis and secretion, motility and chemotaxis as well as cell wall biogenesis. These data give insight into how C. difficile re-establishes its metabolism, re-builds the basic structures of the vegetative cell and resumes growth

Coxiella burnetii Phagocytosis Is Regulated by GTPases of the Rho Family and the RhoA Effectors mDia1 and ROCK

The GTPases belonging to the Rho family control the actin cytoskeleton rearrangements needed for particle internalization during phagocytosis. ROCK and mDia1 are downstream effectors of RhoA, a GTPase involved in that process. Coxiella burnetii, the etiologic agent of Q fever, is internalized by the host´s cells in an actin-dependent manner. Nevertheless, the molecular mechanism involved in this process has been poorly characterized. This work analyzes the role of different GTPases of the Rho family and some downstream effectors in the internalization of C. burnetii by phagocytic and non-phagocytic cells. The internalization of C. burnetii into HeLa and RAW cells was significantly inhibited when the cells were treated with Clostridium difficile Toxin B which irreversibly inactivates members of the Rho family. In addition, the internalization was reduced in HeLa cells that overexpressed the dominant negative mutants of RhoA, Rac1 or Cdc42 or that were knocked down for the Rho GTPases. The pharmacological inhibition or the knocking down of ROCK diminished bacterium internalization. Moreover, C. burnetii was less efficiently internalized in HeLa cells overexpressing mDia1-N1, a dominant negative mutant of mDia1, while the overexpression of the constitutively active mutant mDia1-ΔN3 increased bacteria uptake. Interestingly, when HeLa and RAW cells were infected, RhoA, Rac1 and mDia1 were recruited to membrane cell fractions. Our results suggest that the GTPases of the Rho family play an important role in C. burnetii phagocytosis in both HeLa and RAW cells. Additionally, we present evidence that ROCK and mDia1, which are downstream effectors of RhoA, are involved in that processFil: Salinas Ojeda, Romina Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Ortiz Flores, Rodolfo Matias. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Distel, Jesús Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Aguilera, Milton Osmar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Colombo, Maria Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Beron, Walter. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentin

Statistical Properties of Turbulence: An Overview

We present an introductory overview of several challenging problems in the statistical characterisation of turbulence. We provide examples from fluid turbulence in three and two dimensions, from the turbulent advection of passive scalars, turbulence in the one-dimensional Burgers equation, and fluid turbulence in the presence of polymer additives.Comment: 34 pages, 31 figure

Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding

Pyrrole-imidazole polyamides are a class of small molecules that can be programmed to bind a broad repertoire of DNA sequences, disrupt transcription factor−DNA interfaces, and modulate gene expression pathways in cell culture experiments. In this paper we describe a high-resolution X-ray crystal structure of a β-amino turn-linked eight-ring cyclic Py-Im polyamide bound to the central six base pairs of the sequence d(5′-CCAGTACTGG-3′)_2, revealing significant modulation of DNA shape. We compare the DNA structural perturbations induced by DNA-binding transcripton factors, androgen receptor and glucocorticoid receptor, in the major groove to those induced by cyclic polyamide binding in the minor groove. The cyclic polyamide is an allosteric modulator that perturbs the DNA structure in such a way that nuclear receptor protein binding is no longer compatible. This allosteric perturbation of the DNA helix provides a molecular basis for disruption of transcription factor−DNA interfaces by small molecules, a minimum step in chemical control of gene networks

Particles and fields in fluid turbulence

The understanding of fluid turbulence has considerably progressed in recent years. The application of the methods of statistical mechanics to the description of the motion of fluid particles, i.e. to the Lagrangian dynamics, has led to a new quantitative theory of intermittency in turbulent transport. The first analytical description of anomalous scaling laws in turbulence has been obtained. The underlying physical mechanism reveals the role of statistical integrals of motion in non-equilibrium systems. For turbulent transport, the statistical conservation laws are hidden in the evolution of groups of fluid particles and arise from the competition between the expansion of a group and the change of its geometry. By breaking the scale-invariance symmetry, the statistically conserved quantities lead to the observed anomalous scaling of transported fields. Lagrangian methods also shed new light on some practical issues, such as mixing and turbulent magnetic dynamo.Comment: 165 pages, review article for Rev. Mod. Phy

Clostridium difficile infection in Polish pediatric outpatients with inflammatory bowel disease

The prevalence of Clostridium difficile infection (CDI) in pediatric patients with inflammatory bowel disease (IBD) is still not sufficiently recognized. We assessed the prevalence of CDI and recurrences in outpatients with IBD. In addition, the influence of IBD therapy on CDI and antimicrobial susceptibility of the potentially causative C. difficile strains was assessed. This was a prospective, single-center, observational study. All specimens were obtained between January 2005 and January 2007 from the IBD outpatient service and screened for C. difficile and its toxins. C. difficile isolates were genotyped by PCR ribotyping. Diagnosis of Crohn’s disease (CD) and ulcerative colitis (UC) was based on Porto criteria. Severity of disease was assessed using the Hyams scale (for Crohn’s disease) and the Truelove–Witts scale (for ulcerative colitis). One hundred and forty-three fecal samples from 58 pediatric IBD patients (21 with Crohn’s disease and 37 with ulcerative colitis) were screened. The risk of C. difficile infection was 60% and was independent of disease type (CD or UC) (χ2 = 2.5821, df = 3, p = 0.4606). About 17% of pediatric IBD patients experienced a recurrence of CDI. All C. difficile strains were susceptible to metronidazole, vancomycin and rifampin. A high prevalence of C. difficile infection and recurrences in pediatric outpatients with IBD was observed, independent of disease type. There was no significant correlation between C. difficile infection and IBD therapy. PCR ribotyping revealed C. difficile re-infection and relapses during episodes of IBD in pediatric outpatients