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Damping Function (damping + function)
Selected AbstractsSeed-based systematic discovery of specific transcription factor target genesFEBS JOURNAL, Issue 12 2008Ralf Mrowka Reliable prediction of specific transcription factor target genes is a major challenge in systems biology and functional genomics. Current sequence-based methods yield many false predictions, due to the short and degenerated DNA-binding motifs. Here, we describe a new systematic genome-wide approach, the seed-distribution-distance method, that searches large-scale genome-wide expression data for genes that are similarly expressed as known targets. This method is used to identify genes that are likely targets, allowing sequence-based methods to focus on a subset of genes, giving rise to fewer false-positive predictions. We show by cross-validation that this method is robust in recovering specific target genes. Furthermore, this method identifies genes with typical functions and binding motifs of the seed. The method is illustrated by predicting novel targets of the transcription factor nuclear factor kappaB (NF-,B). Among the new targets is optineurin, which plays a key role in the pathogenesis of acquired blindness caused by adult-onset primary open-angle glaucoma. We show experimentally that the optineurin gene and other predicted genes are targets of NF-,B. Thus, our data provide a missing link in the signalling of NF-,B and the damping function of optineurin in signalling feedback of NF-,B. We present a robust and reliable method to enhance the genome-wide prediction of specific transcription factor target genes that exploits the vast amount of expression information available in public databases today. [source] Evaluation of Smagorinsky-based subgrid-scale models in a finite-volume computationINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 6 2002Petri Majander Abstract Smagorinsky-based models are assessed in a turbulent channel flow simulation at Reb=2800 and Reb=12500. The Navier,Stokes equations are solved with three different grid resolutions by using a co-located finite-volume method. Computations are repeated with Smagorinsky-based subgrid-scale models. A traditional Smagorinsky model is implemented with a van Driest damping function. A dynamic model assumes a similarity of the subgrid and the subtest Reynolds stresses and an explicit filtering operation is required. A top-hat test filter is implemented with a trapezoidal and a Simpson rule. At the low Reynolds number computation none of the tested models improves the results at any grid level compared to the calculations with no model. The effect of the subgrid-scale model is reduced as the grid is refined. The numerical implementation of the test filter influences on the result. At the higher Reynolds number the subgrid-scale models stabilize the computation. An analysis of an accurately resolved flow field reveals that the discretization error overwhelms the subgrid term at Reb=2800 in the most part of the computational domain. Copyright © 2002 John Wiley & Sons, Ltd. [source] Effect of sparse long-chain branching on the step-strain behavior of a series of well-defined polyethylenesPOLYMER ENGINEERING & SCIENCE, Issue 7 2010Christopher D. McGrady The effect of sparse long chain branching, LCB, on the shear step-strain relaxation modulus is analyzed using a series of eight high-density polyethylene (HDPE) resins. Strains of 1 to 1250% are imposed on materials with LCB content ranging from zero to 3.33 LCB per 10,000 carbon atoms. All materials are observed to obey time,strain separation beyond some characteristic time, ,k. The presence of LCB is observed to increase the value of ,k relative to the linear resin. The behavior of the relaxation modulus at times shorter than ,k is investigated by an analysis of the enhancement seen in the linear relaxation modulus, G0(t), as a function of strain and LCB content. This enhancement is seen to (1) increase with increasing strain in all resins, (2) be significantly larger in the sparsely branched HDPE resins relative to the linear HDPE resin, and (3) increase in magnitude with increasing LCB content. The shape and smoothness of the damping function is also investigated. The finite rise time to impose the desired strain is compared to the Rouse relaxation time of linear HDPE resins studied. Sparse LCB is found to increase the magnitude of the relaxation modulus at short times relative to the linear resin. POLYM. ENG. SCI., 2010. © 2010 Society of Plastics Engineers [source] Dynamic stiffness of deep foundations with inclined pilesEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 12 2010L. A. Padrón Abstract The influence of inclined piles on the dynamic response of deep foundations and superstructures is still not well understood and needs further research. For this reason, impedance functions of deep foundations with inclined piles, obtained numerically from a boundary element,finite element coupling model, are provided in this paper. More precisely, vertical, horizontal, rocking and horizontal,rocking crossed dynamic stiffness and damping functions of single inclined piles and 2 × 2 and 3 × 3 pile groups with battered elements are presented in a set of plots. The soil is assumed to be a homogeneous viscoelastic isotropic half-space and the piles are modeled as elastic compressible Euler,Bernoulli beams. The results for different pile group configurations, pile,soil stiffness ratios and rake angles are presented. Copyright © 2010 John Wiley & Sons, Ltd. [source] | ||||||||||