Periodically kicked turbulence

Periodically kicked turbulence is theoretically analyzed within a mean field theory. For large enough kicking strength A and kicking frequency f the Reynolds number grows exponentially and then runs into some saturation. The saturation level can be calculated analytically; different regimes can be observed. For large enough Re we find the saturation level to be proportional to A*f, but intermittency can modify this scaling law. We suggest an experimental realization of periodically kicked turbulence to study the different regimes we theoretically predict and thus to better understand the effect of forcing on fully developed turbulence.Comment: 4 pages, 3 figures. Phys. Rev. E., in pres

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed to minimize false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from ChIP-on-chip data. Biochemically validated analysis in human T-cells reveals that three transcription factor oncogenes, NOTCH1, MYC, and HES1, bind one order of magnitude more promoters than previously thought. Gene expression profiling upon NOTCH1 inhibition shows broad-scale functional regulation across the entire range of predicted target genes, establishing a closer link between occupancy and regulation. Finally, the resolution of a more complete map of transcriptional targets reveals that MYC binds nearly all promoters bound by NOTCH1. Overall, these results suggest an unappreciated complexity of transcriptional regulatory networks and highlight the fundamental importance of genome-scale analysis to represent transcriptional programs

Lognormal scale invariant random measures

In this article, we consider the continuous analog of the celebrated Mandelbrot star equation with lognormal weights. Mandelbrot introduced this equation to characterize the law of multiplicative cascades. We show existence and uniqueness of measures satisfying the aforementioned continuous equation; these measures fall under the scope of the Gaussian multiplicative chaos theory developed by J.P. Kahane in 1985 (or possibly extensions of this theory). As a by product, we also obtain an explicit characterization of the covariance structure of these measures. We also prove that qualitative properties such as long-range independence or isotropy can be read off the equation.Comment: 31 pages; Probability Theory and Related Fields (2012) electronic versio

Dissipative chaotic scattering

We show that weak dissipation, typical in realistic situations, can have a metamorphic consequence on nonhyperbolic chaotic scattering in the sense that the physically important particle-decay law is altered, no matter how small the amount of dissipation. As a result, the previous conclusion about the unity of the fractal dimension of the set of singularities in scattering functions, a major claim about nonhyperbolic chaotic scattering, may not be observable.Comment: 4 pages, 2 figures, revte

Extended Self-similarity in Kinetic Surface Roughening

We show from numerical simulations that a limited mobility solid-on-solid model of kinetically rough surface growth exhibits extended self-similarity analogous to that found in fluid turbulence. The range over which scale-independent power-law behavior is observed is significantly enhanced if two correlation functions of different order, such as those representing two different moments of the difference in height between two points, are plotted against each other. This behavior, found in both one and two dimensions, suggests that the `relative' exponents may be more fundamental than the `absolute' ones.Comment: 4 pages, 4 postscript figures included (some changes made according to referees' comments. accepted for publication in PRE Rapid Communication

Exact Resummations in the Theory of Hydrodynamic Turbulence: I The Ball of Locality and Normal Scaling

This paper is the first in a series of three papers that aim at understanding the scaling behaviour of hydrodynamic turbulence. We present in this paper a perturbative theory for the structure functions and the response functions of the hydrodynamic velocity field in real space and time. Starting from the Navier-Stokes equations (at high Reynolds number Re) we show that the standard perturbative expansions that suffer from infra-red divergences can be exactly resummed using the Belinicher-L'vov transformation. After this exact (partial) resummation it is proven that the resulting perturbation theory is free of divergences, both in large and in small spatial separations. The hydrodynamic response and the correlations have contributions that arise from mediated interactions which take place at some space- time coordinates. It is shown that the main contribution arises when these coordinates lie within a shell of a "ball of locality" that is defined and discussed. We argue that the real space-time formalism developed here offers a clear and intuitive understanding of every diagram in the theory, and of every element in the diagrams. One major consequence of this theory is that none of the familiar perturbative mechanisms may ruin the classical Kolmogorov (K41) scaling solution for the structure functions. Accordingly, corrections to the K41 solutions should be sought in nonperturbative effects. These effects are the subjects of papers II and III in this series, that will propose a mechanism for anomalous scaling in turbulence, which in particular allows multiscaling of the structure functions.Comment: PRE in press, 18 pages + 6 figures, REVTeX. The Eps files of figures will be FTPed by request to [email protected]

Variational bound on energy dissipation in plane Couette flow

We present numerical solutions to the extended Doering-Constantin variational principle for upper bounds on the energy dissipation rate in turbulent plane Couette flow. Using the compound matrix technique in order to reformulate this principle's spectral constraint, we derive a system of equations that is amenable to numerical treatment in the entire range from low to asymptotically high Reynolds numbers. Our variational bound exhibits a minimum at intermediate Reynolds numbers, and reproduces the Busse bound in the asymptotic regime. As a consequence of a bifurcation of the minimizing wavenumbers, there exist two length scales that determine the optimal upper bound: the effective width of the variational profile's boundary segments, and the extension of their flat interior part.Comment: 22 pages, RevTeX, 11 postscript figures are available as one uuencoded .tar.gz file from [email protected]

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification

Motivation: Analyses and algorithmic predictions based on high-throughput data are essential for the success of systems biology in academic and industrial settings. Organizations, such as companies and academic consortia, conduct large multi-year scientific studies that entail the collection and analysis of thousands of individual experiments, often over many physical sites and with internal and outsourced components. To extract maximum value, the interested parties need to verify the accuracy and reproducibility of data and methods before the initiation of such large multi-year studies. However, systematic and well-established verification procedures do not exist for automated collection and analysis workflows in systems biology which could lead to inaccurate conclusions

Exact Resummations in the Theory of Hydrodynamic Turbulence: III. Scenarios for Anomalous Scaling and Intermittency

Elements of the analytic structure of anomalous scaling and intermittency in fully developed hydrodynamic turbulence are described. We focus here on the structure functions of velocity differences that satisfy inertial range scaling laws $S_n(R)\sim R^{\zeta_n}$, and the correlation of energy dissipation $K_{\epsilon\epsilon}(R) \sim R^{-\mu}$. The goal is to understand the exponents $\zeta_n$ and $\mu$ from first principles. In paper II of this series it was shown that the existence of an ultraviolet scale (the dissipation scale $\eta$) is associated with a spectrum of anomalous exponents that characterize the ultraviolet divergences of correlations of gradient fields. The leading scaling exponent in this family was denoted $\Delta$. The exact resummation of ladder diagrams resulted in the calculation of $\Delta$ which satisfies the scaling relation $\Delta=2-\zeta_2$. In this paper we continue our analysis and show that nonperturbative effects may introduce multiscaling (i.e. $\zeta_n$ not being linear in $n$) with the renormalization scale being the infrared outer scale of turbulence $L$. It is shown that deviations from K41 scaling of $S_n(R)$ ($\zeta_n\neq n/3$) must appear if the correlation of dissipation is mixing (i.e. $\mu>0$). We derive an exact scaling relation $\mu = 2\zeta_2-\zeta_4$. We present analytic expressions for $\zeta_n$ for all $n$ and discuss their relation to experimental data. One surprising prediction is that the time decay constant $\tau_n(R)\propto R^{z_n}$ of $S_n(R)$ scales independently of $n$: the dynamic scaling exponent $z_n$ is the same for all $n$-order quantities, $z_n=\zeta_2$.Comment: PRE submitted, 22 pages + 11 figures, REVTeX. The Eps files of figures will be FTPed by request to [email protected]