arXiv subjects

Massimo Vergassola

Publications and source records attributed to Massimo Vergassola.

22 records · Page 2Linked to original sources

arXiv2007

Noise-filtering features of transcription regulation in the yeast S. cerevisiae

Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain specificity for living organisms to be able to elicit specific cellular responses. Specificity stems here from the interplay between binding affinity and cellular abundancy of transcription factor proteins and the binding of such proteins to DNA is thus controlled by their chemical potential. We combine large-scale protein abundance data in the budding yeast with binding affinities for all transcription factors with known DNA binding site sequences to assess the behavior of their chemical potentials. A sizable fraction of transcription factors is apparently bound non-specifically to DNA and the observed abundances are marginally sufficient to ensure high occupations of the functional sites. We argue that a biological cause of this feature is related to its noise-filtering consequences: abundances below physiological levels do not yield significant binding of functional targets and mis-expressions of regulated genes are thus tamed.

q-bio.GN↗

arXiv2004

Active and passive fields face to face

The statistical properties of active and passive scalar fields transported by the same turbulent flow are investigated. Four examples of active scalar have been considered: temperature in thermal convection, magnetic potential in two-dimensional magnetohydrodynamics, vorticity in two-dimensional Ekman turbulence and potential temperature in surface flows. In the cases of temperature and vorticity, it is found that the active scalar behavior is akin to that of its co-evolving passive counterpart. The two other cases indicate that this similarity is in fact not generic and differences between passive and active fields can be striking: in two-dimensional magnetohydrodynamics the magnetic potential performs an inverse cascade while the passive scalar cascades toward the small-scales; in surface flows, albeit both perform a direct cascade, the potential temperature and the passive scalar have different scaling laws already at the level of low-order statistical objects. These dramatic differences are rooted in the correlations between the active scalar input and the particle trajectories. The role of such correlations in the issue of universality in active scalar transport and the behavior of dissipative anomalies is addressed.

nlin.CD↗

arXiv2001

Scaling and universality in turbulent convection

Anomalous correlation functions of the temperature field in two-dimensional turbulent convection are shown to be universal with respect to the choice of external sources. Moreover, they are equal to the anomalous correlations of the concentration field of a passive tracer advected by the convective flow itself. The statistics of velocity differences is found to be universal, self-similar and close to Gaussian. These results point to the conclusion that temperature intermittency in two-dimensional turbulent convection may be traced back to the existence of statistically preserved structures, as it is in passive scalar turbulence.

nlin.CD↗

arXiv1998

Phase Transition in the Passive Scalar Advection

The paper studies the behavior of the trajectories of fluid particles in a compressible generalization of the Kraichnan ensemble of turbulent velocities. We show that, depending on the degree of compressibility, the trajectories either explosively separate or implosively collapse. The two behaviors are shown to result in drastically different statistical properties of scalar quantities passively advected by the flow. At weak compressibility, the explosive separation of trajectories induces a familiar direct cascade of the energy of a scalar tracer with a short-distance intermittency and dissipative anomaly. At strong compressibility, the implosive collapse of trajectories leads to an inverse cascade of the tracer energy with suppressed intermittency and with the energy evacuated by large scale friction. A scalar density whose advection preserves mass exhibits in the two regimes opposite cascades of the total mass squared. We expect that the explosive separation and collapse of Lagrangian trajectories occur also in more realistic high Reynolds number velocity ensembles and that the two phenomena play a crucial role in fully developed turbulence.

cond-mat↗