Polymers in linear shear flow: a numerical study

We study the dynamics of a single polymer subject to thermal fluctuations in a linear shear flow. The polymer is modeled as a finitely extendable nonlinear elastic FENE dumbbell. Both orientation and elongation dynamics are investigated numerically as a function of the shear strength, by means of a new efficient integration algorithm. The results are in agreement with recent experiments.Comment: 7 pages, see also the preceding paper (http://arxiv.org/nlin.CD/0503028

Dynamics of threads and polymers in turbulence: power-law distributions and synchronization

We study the behavior of threads and polymers in a turbulent flow. These objects have finite spatial extension, so the flow along them differs slightly. The corresponding drag forces produce a finite average stretching and the thread is stretched most of the time. Nevertheless, the probability of shrinking fluctuations is significant and is known to decay only as a power-law. We show that the exponent of the power law is a universal number independent of the statistics of the flow. For polymers the coil-stretch transition exists: the flow must have a sufficiently large Lyapunov exponent to overcome the elastic resistance and stretch the polymer from the coiled state it takes otherwise. The probability of shrinking from the stretched state above the transition again obeys a power law but with a non-universal exponent. We show that well above the transition the exponent becomes universal and derive the corresponding expression. Furthermore, we demonstrate synchronization: the end-to-end distances of threads or polymers above the transition are synchronized by the flow and become identical. Thus, the transition from Newtonian to non-Newtonian behavior in dilute polymer solutions can be seen as an ordering transition.Comment: 13 pages, version accepted to Journal of Statistical Mechanic

Elastic turbulence in curvilinear flows of polymer solutions

Following our first report (A. Groisman and V. Steinberg, \sl Nature $\bf 405$, 53 (2000)) we present an extended account of experimental observations of elasticity induced turbulence in three different systems: a swirling flow between two plates, a Couette-Taylor (CT) flow between two cylinders, and a flow in a curvilinear channel (Dean flow). All three set-ups had high ratio of width of the region available for flow to radius of curvature of the streamlines. The experiments were carried out with dilute solutions of high molecular weight polyacrylamide in concentrated sugar syrups. High polymer relaxation time and solution viscosity ensured prevalence of non-linear elastic effects over inertial non-linearity, and development of purely elastic instabilities at low Reynolds number (Re) in all three flows. Above the elastic instability threshold, flows in all three systems exhibit features of developed turbulence. Those include: (i)randomly fluctuating fluid motion excited in a broad range of spatial and temporal scales; (ii) significant increase in the rates of momentum and mass transfer (compared to those expected for a steady flow with a smooth velocity profile). Phenomenology, driving mechanisms, and parameter dependence of the elastic turbulence are compared with those of the conventional high Re hydrodynamic turbulence in Newtonian fluids.Comment: 23 pages, 26 figure

Fundamental scaling laws of on-off intermittency in a stochastically driven dissipative pattern forming system

Noise driven electroconvection in sandwich cells of nematic liquid crystals exhibits on-off intermittent behaviour at the onset of the instability. We study laser scattering of convection rolls to characterize the wavelengths and the trajectories of the stochastic amplitudes of the intermittent structures. The pattern wavelengths and the statistics of these trajectories are in quantitative agreement with simulations of the linearized electrohydrodynamic equations. The fundamental $\tau^{-3/2}$ distribution law for the durations $\tau$ of laminar phases as well as the power law of the amplitude distribution of intermittent bursts are confirmed in the experiments. Power spectral densities of the experimental and numerically simulated trajectories are discussed.Comment: 20 pages and 17 figure

The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response

The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1Δ cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant. Importantly, a significant number of the mRNAs encoding these targets were also identified as Slf1p-mRNA targets. We show that Slf1p remains associated with the few translating ribosomes following hydrogen peroxide stress and that Slf1p co-immunoprecipitates ribosomes and members of the eIF4E/eIF4G/Pab1p ‘closed loop’ complex suggesting that Slf1p interacts with actively translated mRNAs following stress. Finally, mutational analysis of SLF1 revealed a novel ribosome interacting domain in Slf1p, independent of its RNA binding La-motif. Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control

Study of dose-dependent actoprotective effect of ATACL on physical performancend psychoemotional status of animals under exhausting exercise

The aim of the study was to investigate the dose-dependent actoprotective effect of ATACL on physical performance and psychoemotional status of animals under conditions of exhausting exercis

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses

BACKGROUND: Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5' cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with individual mRNAs likely contribute to differences in translation initiation frequencies between mRNAs. As translation initiation is globally reprogrammed by environmental stresses, we were interested in determining whether eIF4F interactions with individual mRNAs are reprogrammed and how this may contribute to global environmental stress responses. RESULTS: Using a tagged-factor protein capture and RNA-sequencing (RNA-seq) approach, we have assessed how mRNA associations with eIF4E, eIF4G1 and eIF4G2 change globally in response to three defined stresses that each cause a rapid attenuation of protein synthesis: oxidative stress induced by hydrogen peroxide and nutrient stresses caused by amino acid or glucose withdrawal. We find that acute stress leads to dynamic and unexpected changes in eIF4F-mRNA interactions that are shared among each factor and across the stresses imposed. eIF4F-mRNA interactions stabilised by stress are predominantly associated with translational repression, while more actively initiating mRNAs become relatively depleted for eIF4F. Simultaneously, other mRNAs are insulated from these stress-induced changes in eIF4F association. CONCLUSION: Dynamic eIF4F-mRNA interaction changes are part of a coordinated early translational control response shared across environmental stresses. Our data are compatible with a model where multiple mRNA closed-loop complexes form with differing stability. Hence, unexpectedly, in the absence of other stabilising factors, rapid translation initiation on mRNAs correlates with less stable eIF4F interactions