117 research outputs found
Object oriented tools for scientific computing
No full textA set of object oriented tools is presented which, when combined, yield an efficient parallel finite element program. Special emphasis is given to details within the concept of the tools which enhance their efficiency. The experience of the author has shown that the design concepts documented are crucial for the efficiency of the issuing code, and that they can easily be incorporated within existing object oriented programs.161637
Object oriented design philosophy for scientific computing
No full textThis contribution gives an overview of current research in applying object oriented programming to scientific computing at the computational mechanics laboratory (LABMEC) at the school of civil engineering - UNICAMP. The main goal of applying object oriented programming to scientific computing is to implement increasingly complex algorithms in a structured manner and to hide the complexity behind a simple user interface. The following areas are current topics of research and documented within the paper: hp-adaptive finite elements in one-, two- and three dimensions with the development of automatic refinement strategies, multigrid methods applied to adaptively refined finite element solution spaces and parallel computing.36579380
Systematic and generic construction of shape functions for p-adaptive meshes of multidimensional finite elements
No full textThis paper presents a methodology for generating high-order shape functions for the complete family of finite elements. The geometric entities presented are the point, line, triangle, quadrilateral, tetrahedron. pyramid, prism, and hexahedron. The shape functions constructed are hierarchical and generate continuous approximation spaces. The order of interpolation of the shape function can be determined independently for each edge, face, and volume. The space of interpolation of order p for each element is complete. This definition allows for the construction of hybrid meshes with any combination of these elements, including elements of distinct dimension and/or interpolation order. The reader will observe that our systematic way of constructing shape functions can be extended to elements of higher-dimension. (C) 2009 Elsevier B.V. All rights reserved.19821-261716172
A new procedure for the construction of hierarchical high order Hdiv and Hcurl finite element spaces
No full textConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)This paper considers a systematic procedure for the construction of a hierarchy of high order finite element approximation for Hdiv and Hcurl spaces based on triangular and quadrilateral partitions of bidimensional domains. The principle is to choose an appropriate set of vectors, based on the geometry of each element, which are multiplied by an available set of H-1 hierarchical scalar basic functions. This strategy produces vector basis functions with continuous normal or tangent components on the elements interfaces, properties that characterise functions in Hdiv or Hcurl, respectively. We also present a numerical study to evaluate the correct balancedness of the resulting Hdiv spaces of degree k and L-2 spaces of degree k - 1 on the resolution of the mixed formulation for a Steklov eigenvalue problem. (c) 2012 Elsevier B.V. All rights reserved.240SI204214Brazilian National Agency of Petroleum, Natural Gas and Biofuels (ANP - PETROBRAS)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq
Stabilized discontinuous Galerkin method for hyperbolic equations
No full textIn this work a new stabilization technique is proposed and studied for the discontinuous Galerkin method applied to hyperbolic equations. In order to avoid the use of slope limiters, a streamline diffusion-like term is added to control oscillations for arbitrary element orders. Thus, the scheme combines ideas from both the Runge-Kutta discontinuous Galerkin method [J. Scient. Comput. 16 (2001) 173] and the streamline diffusion method [Comput. Methods Appl. Mech. Engrg. 32 (1982)]. To increase the stability range of the method, the diffusion term is treated implicitly. The result is a scheme with higher order in space with the same stability range as the finite volume method. An optimal relation between the time step and the size of the diffusion coefficient is analyzed for numerical precision. The scheme is implemented using the object oriented programming philosophy based on the environment described in [Comput. Methods Appl. Mech. Engrg. 150 (1997)]. Accuracy and shock capturing abilities of the method are analyzed in terms of two bidimensional model problems: the rotating cone and the backward facing step problem for the Euler equations of gas dynamics. (c) 2004 Elsevier B.V. All rights reserved.194171861187
5-Aza-2 '-deoxycytidine reactivates gene expression via degradation of pRb pocket proteins
No full textNot only does 5-aza-2'-deoxycytidine (5-aza-CdR) induce the reexpression of silenced genes through the demethylation of CpG islands, but it increases the expression of unmethylated genes. However, the mechanism by which 5-aza-CdR activates the expression of genes is not completely understood. Here, we report that the pRb pocket proteins pRb, p107, and p130 were degraded in various cancer cell lines in response to 5-aza-CdR treatment, and this effect was dependent on the proteasome pathway. Mouse double minute 2 (MDM2) played a critical role in this 5-aza-CdR-induced degradation of pRb. Furthermore, PP2A phosphatase-induced MDM2 dephosphorylation at S260 was found to be essential for MDM2 binding to pRb in the presence of 5-aza-CdR. pRb degradation resulted in the significant reexpression of several genes, including methylated CDKN2A, RASFF1A, and unmethylated CDKN2D. Finally, knockdown of pRb pocket proteins by either RNAi or 5-aza-CdR treatment induced a significant decrease in the recruitment of SUV39H1 and an increase in the enrichment of KDM3B and KDM4A to histones around the promoter of RASFF1A and thus reduced H3K9 di- and trimethylation, by which RASFF1A expression is activated. Our data reveal a novel mechanism by which 5-aza-CdR induces the expression of both methylated and unmethylated genes by degrading pRb pocket proteins.-Zheng, Z., Li, L., Liu, X., Wang, D., Tu, B., Wang, L., Wang, H., Zhu, W.-G. 5-Aza-2'-deoxycytidine reactivates gene expression via degradation of pRb pocket proteins. FASEB J. 26, 449-459 (2012). www.fasebj.orghttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000299202200044&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Biochemistry & Molecular BiologyBiologyCell BiologySCI(E)PubMed12ARTICLE1449-4592
A combined continuous-discontinuous finite element method for convection-diffusion problems
No full textDiscontinuous Galerkin (DGM) method combines the advantages of stability of finite volume method and the accuracy of continuous finite element method (FEIVI). Applications of the DGM are particularly valuable where the solution presents high-gradients or discontinuities, such as boundary layers and shock problems. A disadvantage of the DGM is the higher computational cost when comparing to classic finite element method, due to the increased number of degrees of freedom. With this motivation, in this paper we explore the idea of combining continuous and discontinuous Galerkin formulations for the simulation of convection-diffusion problems. The computational domain is decomposed into two parts. In one region the solution is supposed to be smooth, and the traditional continuous finite element method is applied. On the other hand, where steep gradients are expected, we use a, discontinuous Galerkin formulation. This paper presents numerical results for the combined FEM/DGM method applied to convection-diffusion problems.4322924
A goal-oriented hp-adaptive discontinuous Galerkin approach for biharmonic problems
No full textConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)A goal-oriented algorithm is developed and applied for hp-adaptive approximations given by the discontinuous Galerkin finite element method for the biharmonic equation. The methodology is based on the dual problem associated with the target functional. We consider three error estimators and analyse their properties as basic tools for the design of the hp-adaptive algorithm. To improve adaptation, the combination of two different error estimators is used, each one at its best efficiency, to guide the tasks of where and how to adapt the approximation spaces. The performance of the resulting hp-adaptive schemes is illustrated by numerical experiments for two benchmark problems. Copyright (c) 2013 John Wiley & Sons, Ltd.974274297Brazilian National Agency of Petroleum, Natural Gas and Biofuels (ANP - PETROBRAS)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP
Modelling of Metastable Equilibrium State using PRB Principles
No full textThis thesis proposes the introduction of a metastable equilibrium state in a viscoelastic pre-curved beam. Generally, metamaterials with bistable unit cells need an external application of force to restore, leading to the contemplation of possible structures with self restorable behaviour. Such restorable nature is associated with metastable equilibrium, which is a time-dependent equilibrium state. The objective of the topic is to build a proof of concept for metastability in a pre-curved beam and identify the influence of geometric parameters on metastability. In the course of the thesis, various models of bistable designs are classified. A feasible bistable mechanism was selected, and the metastable nature is introduced through viscoelasticity. In this thesis, an analytical model is formulated by combining an equivalent Pseudo Rigid Body (PRB) model of the pre-curved beam (modelling the beam's compliance) with Standard Linear Solid (SLS) model (modelling the beam’s viscoelasticity). Prototypes are manufactured by using FDM printing of TPU material. Experimental studies are performed for the evaluation of material properties and testing for metastability in pre-curved beams with various shape factors. The results of experimental studies proved the possibility of metastable equilibrium in viscoelastic pre-curved beams. Later, discussions are offered to improve the predictability of metastability in pre-curved beams and the scope for future studies
Aqua regia digestible and labile metal concentrations of PRB media
No full textProgress Code: completedStatement: Data are fine. Samples were diluted and rerun if concentrations were above the method calibration curve.The data set consists of two types of assessments of permeable reactive barrier (PRB) media: aqua regia digestions and 1 M HCl acid extractions. All analytical analysis was completed using inductively couple plasma-optical emission spectroscopy (ICP-OES).<br/><br/>Aqua regia digestions were conducted on to assess the purity of three iron sources (Peerless, Connelly and Chem-Supply). 15 mL of aqua regia (3:1 concentrated hydrochloric acid: nitric acid) was added to 0.5 g iron samples in triplicated Teflon containers. The solution was heated at 80 degrees C for three hours and left at 40 degrees C for a further three days. The mixture was diluted to 100 mL and filtered at 0.45 microns before analysis. <br/><br/>The Lower PRB at the Casey Main Power House was originally constructed in the 2005/06 summer for details refer to (Mumford et al., 2013). The reactive gate consists of five modified Australian Antarctic Division cage pallets with external dimensions 1.8 x L 1.1 W x 0.75 H m. During the 2012/13 field season, media in the fifth cage was replaced with a new trial media sequence (Statham draft publication). Refilling occurred on the 16th of January. In this process mixed media sequences were homogenised by a cement mixer in 40 L batches and then placed in the PRB cage.<br/><br/>Material samples were cored from within the new media sequence of the PRB, three in GAC/ZeoPro, three in ZVI/sand and two in the zeolite section (Statham unpublished manuscript). All samples were collected from a depth of 45-60 cm then stored at -18 degrees C for transport to Australia. The concentration of bioavailable metals within the field and raw material samples were using a method recommended by Snape et al. (2004). All extractions used 2 g of oven dried medium and 40 mL of HCl solution and were conducted in new duplicated polypropylene containers. The mixtures were revolved on a suspension mixer for four hours, promptly filtered at 0.45 microns before analysis <br/><br/>Element concentrations were determined by ICP-OES using a Varian 720-ES spectrometer at the Australian Antarctic Division. The emission intensity of standards and sample solutions was measured following 1:1 in-line mixing with a solution of 0.75% (w/v) CsCl matrix modifier in 10% (v/v) HNO3 containing 5 mg L-1 yttrium as an internal standard. Aqua regia iron concentrations were determined from a 1 in 50 dilution of the filtered solution. The matrix modifier was deemed unnecessary for the HCl extractions. A blank samples for both methods indicated that the presence of the analysed elements was due to dissolution from PRB media and not other sources.<br/><br/>The limit of quantification (LOQ) was determined by the NATA extrapolation method (NATA, 2009) using concentrations of 20, 50 and 100 microns L-1 for phosphorus and potassium and 4, 10 and 20 microns L-1 for all other measured elements. <br/><br/>The data consists of four excel files of ICP analysis results:<br/>1. The limit of quantification and certified reference material results from aqua regia digestion<br/>2. The limit of quantification and certified reference material results from 1 M HCl extractions<br/>3. Aqua regia digestion results and calculations<br/>4. 1 M HCl extractions results and calculation
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