Self-organized escape of oscillator chains in nonlinear potentials

We present the noise free escape of a chain of linearly interacting units from a metastable state over a cubic on-site potential barrier. The underlying dynamics is conservative and purely deterministic. The mutual interplay between nonlinearity and harmonic interactions causes an initially uniform lattice state to become unstable, leading to an energy redistribution with strong localization. As a result a spontaneously emerging localized mode grows into a critical nucleus. By surpassing this transition state, the nonlinear chain manages a self-organized, deterministic barrier crossing. Most strikingly, these noise-free, collective nonlinear escape events proceed generally by far faster than transitions assisted by thermal noise when the ratio between the average energy supplied per unit in the chain and the potential barrier energy assumes small values

Gravitational Lensing as Signal and Noise in Lyman-alpha Forest Measurements

In Lyman-alpha forest measurements it is generally assumed that quasars are mere background light sources which are uncorrelated with the forest. Gravitational lensing of the quasars violates this assumption. This effect leads to a measurement bias, but more interestingly it provides a valuable signal. The lensing signal can be extracted by correlating quasar magnitudes with the flux power spectrum and with the flux decrement. These correlations will be challenging to measure but their detection provides a direct measure of how features in the Lyman-alpha forest trace the underlying mass density field. Observing them will test the fundamental hypothesis that fluctuations in the forest are predominantly driven by fluctuations in mass, rather than in the ionizing background, helium reionization or winds. We discuss ways to disentangle the lensing signal from other sources of such correlations, including dust, continuum and background residuals. The lensing-induced measurement bias arises from sample selection: one preferentially collects spectra of magnified quasars which are behind overdense regions. This measurement bias is ~0.1-1% for the flux power spectrum, optical depth and the flux probability distribution. Since the effect is systematic, quantities such as the amplitude of the flux power spectrum averaged across scales should be interpreted with care.Comment: 22 pages, 8 figures; v2: references added, discussion expanded, matches PRD accepted versio

Galaxy-Quasar correlations between APM galaxies and Hamburg-ESO QSOs

We detect angular galaxy-QSO cross-correlations between the APM Galaxy Catalogue and a preliminary release (consisting of roughly half of the anticipated final catalogue) of the Hamburg-ESO Catalogue of Bright QSOs as a function of source QSO redshift using multiple cross-correlation estimators. Each of the estimators yield very similar results, implying that the APM catalogue and the Hamburg-ESO survey are both fair samples of the respective true galaxy and QSO populations. Though the signal matches the expectations of gravitational lensing qualitatively, the strength of the measured cross-correlation signal is significantly greater than the CDM models of lensing by large scale structure would suggest. This same disagreement between models and observation has been found in several earlier studies. We estimate our confidence in the correlation detections versus redshift by generating 1000 random realizations of the Hamburg-ESO QSO survey: We detect physical associations between galaxies and low-redshift QSOs at 99% confidence and detect lensing associations at roughly 95% confidence for QSOs with redshifts between 0.6 and 1. Control cross-correlations between Galactic stars and QSOs show no signal. Finally, the overdensities (underdensities) of galaxies near QSO positions relative to those lying roughly 135 - 150 arcmin away are uncorrelated with differences in Galactic extinction between the two regions, implying that Galactic dust is not significantly affecting the QSO sample.Comment: 35 pages total, including 9 figures. Accepted by the Astrophysical Journa

Resonance-like phenomena of the mobility of a chain of nonlinear coupled oscillators in a two-dimensional periodic potential

We study the Langevin dynamics of a two-dimensional discrete oscillator chain absorbed on a periodic substrate and subjected to an external localized point force. Going beyond the commonly used harmonic bead-spring model, we consider a nonlinear Morse interaction between the next-nearest-neighbors. We focus interest on the activation of directed motion instigated by thermal fluctuations and the localized point force. In this context the local transition states are identified and the corresponding activation energies are calculated. As a novel feature it is found that the transport of the chain in point force direction is determined by stepwise escapes of a single unit or segments of the chain due to the existence of multiple locally stable attractors. The non-vanishing net current of the chain is quantitatively assessed by the value of the mobility of the center of mass. It turns out that the latter as a function of the ratio of the competing length scales of the system, that is the period of the substrate potential and the equilibrium distance between two chain units, shows a resonance behavior. More precisely there exist a set of optimal parameter values maximizing the mobility. Interestingly, the phenomenon of negative resistance is found, i.e. the mobility possesses a minimum at a finite value of the strength of the thermal fluctuations for a given overcritical external driving force.Comment: 25 pages, 12 figure

Thermal Degradation of Adsorbed Bottle-Brush Macromolecules: Molecular Dynamics Simulation

The scission kinetics of bottle-brush molecules in solution and on an adhesive substrate is modeled by means of Molecular Dynamics simulation with Langevin thermostat. Our macromolecules comprise a long flexible polymer backbone with $L$ segments, consisting of breakable bonds, along with two side chains of length $N$, tethered to each segment of the backbone. In agreement with recent experiments and theoretical predictions, we find that bond cleavage is significantly enhanced on a strongly attractive substrate even though the chemical nature of the bonds remains thereby unchanged. We find that the mean bond life time decreases upon adsorption by more than an order of magnitude even for brush molecules with comparatively short side chains $N=1 \div 4$. The distribution of scission probability along the bonds of the backbone is found to be rather sensitive regarding the interplay between length and grafting density of side chains. The life time declines with growing contour length $L$ as $\propto L^{-0.17}$, and with side chain length as $\propto N^{-0.53}$. The probability distribution of fragment lengths at different times agrees well with experimental observations. The variation of the mean length $L(t)$ of the fragments with elapsed time confirms the notion of the thermal degradation process as a first order reaction.Comment: 15 pages, 7 figure

A Novel Unsupervised Method to Identify Genes Important in the Anti-viral Response: Application to Interferon/Ribavirin in Hepatitis C Patients

Background: Treating hepatitis C with interferon/ribavirin results in a varied response in terms of decrease in viral titer and ultimate outcome. Marked responders have a sharp decline in viral titer within a few days of treatment initiation, whereas in other patients there is no effect on the virus (poor responders). Previous studies have shown that combination therapy modifies expression of hundreds of genes in vitro and in vivo. However, identifying which, if any, of these genes have a role in viral clearance remains challenging. Aims: The goal of this paper is to link viral levels with gene expression and thereby identify genes that may be responsible for early decrease in viral titer. Methods: Microarrays were performed on RNA isolated from PBMC of patients undergoing interferon/ribavirin therapy. Samples were collected at pre-treatment (day 0), and 1, 2, 7, 14 and 28 days after initiating treatment. A novel method was applied to identify genes that are linked to a decrease in viral titer during interferon/ribavirin treatment. The method uses the relationship between inter-patient gene expression based proximities and inter-patient viral titer based proximities to define the association between microarray gene expression measurements of each gene and viral-titer measurements. Results: We detected 36 unique genes whose expressions provide a clustering of patients that resembles viral titer based clustering of patients. These genes include IRF7, MX1, OASL and OAS2, viperin and many ISG's of unknown function. Conclusion: The genes identified by this method appear to play a major role in the reduction of hepatitis C virus during the early phase of treatment. The method has broad utility and can be used to analyze response to any group of factors influencing biological outcome such as antiviral drugs or anti-cancer agents where microarray data are available. © 2007 Brodsky et al

Analysis of Mice Lacking DNaseI Hypersensitive Sites at the 5′ End of the IgH Locus

The 5′ end of the IgH locus contains a cluster of DNaseI hypersensitive sites, one of which (HS1) was shown to be pro-B cell specific and to contain binding sites for the transcription factors PU.1, E2A, and Pax5. These data as well as the location of the hypersensitive sites at the 5′ border of the IgH locus suggested a possible regulatory function for these elements with respect to the IgH locus. To test this notion, we generated mice carrying targeted deletions of either the pro-B cell specific site HS1 or the whole cluster of DNaseI hypersensitive sites. Lymphocytes carrying these deletions appear to undergo normal development, and mutant B cells do not exhibit any obvious defects in V(D)J recombination, allelic exclusion, or class switch recombination. We conclude that deletion of these DNaseI hypersensitive sites does not have an obvious impact on the IgH locus or B cell development

Inheritance of an Epigenetic Mark: The CpG DNA Methyltransferase 1 Is Required for De Novo Establishment of a Complex Pattern of Non-CpG Methylation

Site-specific methylation of cytosines is a key epigenetic mark of vertebrate DNA. While a majority of the methylated residues are in the symmetrical (meC)pG:Gp(meC) configuration, a smaller, but significant fraction is found in the CpA, CpT and CpC asymmetric (non-CpG) dinucleotides. CpG methylation is reproducibly maintained by the activity of the DNA methyltransferase 1 (Dnmt1) on the newly replicated hemimethylated substrates (meC)pG:GpC. On the other hand, establishment and hereditary maintenance of non-CpG methylation patterns have not been analyzed in detail. We previously reported the occurrence of site- and allele-specific methylation at both CpG and non-CpG sites. Here we characterize a hereditary complex of non-CpG methylation, with the transgenerational maintenance of three distinct profiles in a constant ratio, associated with extensive CpG methylation. These observations raised the question of the signal leading to the maintenance of the pattern of asymmetric methylation. The complete non-CpG pattern was reinstated at each generation in spite of the fact that the majority of the sperm genomes contained either none or only one methylated non-CpG site. This observation led us to the hypothesis that the stable CpG patterns might act as blueprints for the maintenance of non-CpG DNA methylation. As predicted, non-CpG DNA methylation profiles were abrogated in a mutant lacking Dnmt1, the enzymes responsible for CpG methylation, but not in mutants defective for either Dnmt3a or Dnmt2

Probing the Universe with Weak Lensing

Gravitational lenses can provide crucial information on the geometry of the Universe, on the cosmological scenario of formation of its structures as well as on the history of its components with look-back time. In this review, I focus on the most recent results obtained during the last five years from the analysis of the weak lensing regime. The interest of weak lensing as a probe of dark matter and the for study of the coupling between light and mass on scales of clusters of galaxies, large scale structures and galaxies is discussed first. Then I present the impact of weak lensing for the study of distant galaxies and of the population of lensed sources as function of redshift. Finally, I discuss the potential interest of weak lensing to constrain the cosmological parameters, either from pure geometrical effects observed in peculiar lenses, or from the coupling of weak lensing with the CMB.Comment: To appear Annual Review of Astronomy and Astrophysiscs Vol. 37. Latex and psfig.sty. Version without figure, 54 pages, 73Kb. Complete version including 13 figures (60 pages) available on ftp.iap.fr anonymous account in /pub/from_users/mellier/AnnualReview ; file ARAAmellier.ps.gz 1.6 M