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See detailEvaluating the effects of information reliability on travellers’ route choice
Bifulco, Gennaro N.; Di Pace, Roberta; Viti, Francesco UL

in European Transport Research Review (2013)

Purpose This paper analyses travellers’ behaviour with respect to route choice in a context where an Advanced Traveller Information System (ATIS) is in place. ATIS are important applications in the field ... [more ▼]

Purpose This paper analyses travellers’ behaviour with respect to route choice in a context where an Advanced Traveller Information System (ATIS) is in place. ATIS are important applications in the field of intelligent transportation systems (ITS). However, the practical impact of ATIS is still a matter for debate, and identification of expected route choice behaviour under ATIS is one of themain ways to assess their practical importance. Methods Travellers’ choices are frequently explored by means of stated preference (SP) approaches. In this paper we discuss some issues to be addressed when an SP survey is carried out, with particular reference to cases where a repeated choice approach is employed in the survey. Results Our analysis concerns an application of the SP approach in a pilot study aimed at identifying the effects of ATIS accuracy on travellers’ compliance with information. Conclusions This paper aims tomake two major contributions. First of all, empirical analyses based on proper indicators and statistical tests are suggested in order to evaluate how the collected data have to be handled in order to eliminate transient route-choice observations. These are due to the warm-up phase inherently associated with the survey method adopted, dealing with repeated choices. Secondly, we analyse (stationary) route choice in order to assess the effects of information reliability (and the kind of information) on both route choice and compliance. [less ▲]

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See detailCalibration of a microscopic simulation model for emission calculation
Li, Jie; Van Zuylen, Henk J.; Chen, Yusen et al

in Transportation Research. Part C : Emerging Technologies (2013), 31

Emissions by road traffic can be reduced by optimising traffic control. The impact of this optimisation on emission can be analysed ex ante by simulation. The simulation programs used for this analysis ... [more ▼]

Emissions by road traffic can be reduced by optimising traffic control. The impact of this optimisation on emission can be analysed ex ante by simulation. The simulation programs used for this analysis should be valid with respect to the traffic characteristics that determine the emissions. Thus calibration of the parameters is a prerequisite. In most cases, volumes, travel times and queues are used to calibrate simulation models, rather than detailed driving characteristics such as speed and acceleration patterns. However, these driving behaviour parameters determine the vehicular emissions to a great extent. A study was carried out in which the driving behaviour parameters in a microscopic simulation model (VISSIM) were calibrated using real trajectories collected by image processing at an intersection in Rotterdam. The sensitivity of the simulation results for driving behaviour parameters was investigated. The most influential parameters were identified and adjusted to ensure that the simulation results were consistent with the observed traffic and could provide valid estimations of the total production of emissions. [less ▲]

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See detailDynamic OD estimation in congested networks: theoretical findings and implications in practice
Frederix, Rodric; Viti, Francesco UL; Tampere, Chris M.J.

in Transportmetrica (2013), 9(6), 494-513

In this study we analyse the impact of congestion in dynamic origin–destination (OD) estimation. This problem is typically expressed using a bi-level formulation. When solving this problem the ... [more ▼]

In this study we analyse the impact of congestion in dynamic origin–destination (OD) estimation. This problem is typically expressed using a bi-level formulation. When solving this problem the relationship between OD flows and link flows is linearised. In this article the effect of using two types of linear relationship on the estimation process is analysed. It is shown that one type of linearisation implicitly assumes separability of the link flows, which can lead to biased results when dealing with congested networks. Advantages and disadvantages of adopting non-separable relationships are discussed. Another important source of error attributable to congestion dynamics is the presence of local minima in the objective function. It is illustrated that these local minima are the result of an incorrect interpretation of the information from the detectors. The theoretical findings are cast into a new methodology, which is successfully tested in a proof of concept. [less ▲]

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See detailXLME interpolants, a seamless bridge between XFEM and enriched meshless methods
Amiri, F.; Anitescu, C.; Arroyo, M. et al

in Computational Mechanics (2013)

In this paper, we develop a method based on local maximum entropy shape functions together with enrichment functions used in partition of unity methods to discretize problems in linear elastic fracture ... [more ▼]

In this paper, we develop a method based on local maximum entropy shape functions together with enrichment functions used in partition of unity methods to discretize problems in linear elastic fracture mechanics. We obtain improved accuracy relative to the standard extended finite element method at a comparable computational cost. In addition, we keep the advantages of the LME shape functions, such as smoothness and non-negativity. We show numerically that optimal convergence (same as in FEM) for energy norm and stress intensity factors can be obtained through the use of geometric (fixed area) enrichment with no special treatment of the nodes near the crack such as blending or shifting. © 2013 Springer-Verlag Berlin Heidelberg. [less ▲]

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See detailCertification of projection-based reduced order modelling in computational homogenisation by the constitutive relation error
Kerfriden, P.; Ródenas, J. J.; Bordas, Stéphane UL

in International Journal for Numerical Methods in Engineering (2013)

SUMMARY: In this paper, we propose upper and lower error bounding techniques for reduced order modelling applied to the computational homogenisation of random composites. The upper bound relies on the ... [more ▼]

SUMMARY: In this paper, we propose upper and lower error bounding techniques for reduced order modelling applied to the computational homogenisation of random composites. The upper bound relies on the construction of a reduced model for the stress field. Upon ensuring that the reduced stress satisfies the equilibrium in the finite element sense, the desired bounding property is obtained. The lower bound is obtained by defining a hierarchical enriched reduced model for the displacement. We show that the sharpness of both error estimates can be seamlessly controlled by adapting the parameters of the corresponding reduced order model. © 2013 John Wiley & Sons, Ltd. [less ▲]

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See detailVibration of functionally graded material plates with cutouts & cracks in thermal environment
Rahimabadi, A. A.; Natarajan, S.; Bordas, Stéphane UL

in Key Engineering Materials (2013), 560

In this paper, the effect of a centrally located cutout (circular and elliptical) and cracks emanating from the cutout on the free flexural vibration behaviour of functionally graded material plates in ... [more ▼]

In this paper, the effect of a centrally located cutout (circular and elliptical) and cracks emanating from the cutout on the free flexural vibration behaviour of functionally graded material plates in thermal environment is studied. The discontinuity surface is represented independent of the mesh by exploiting the partition of unity method framework. A Heaviside function is used to capture the jump in the displacement across the discontinuity surface and asymptotic branch functions are used to capture the singularity around the crack tip. An enriched shear flexible 4-noded quadrilateral element is used for the spatial discretization. The properties are assumed to vary only in the thickness direction. The effective properties of the functionally graded material are estimated using the Mori-Tanaka homogenization scheme and the plate kinematics is based on the first order shear deformation theory. The influence of the plate geometry, the geometry of the cutout, the crack length, the thermal gradient and the boundary conditions on the free flexural vibration is numerically studied. © (2013) Trans Tech Publications, Switzerland. [less ▲]

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See detailMesh adaptivity driven by goal-oriented locally equilibrated superconvergent patch recovery
González-Estrada, O. A.; Nadal, E.; Ródenas, J. J. et al

in Computational Mechanics (2013)

Goal-oriented error estimates (GOEE) have become popular tools to quantify and control the local error in quantities of interest (QoI), which are often more pertinent than local errors in energy for ... [more ▼]

Goal-oriented error estimates (GOEE) have become popular tools to quantify and control the local error in quantities of interest (QoI), which are often more pertinent than local errors in energy for design purposes (e.g. the mean stress or mean displacement in a particular area, the stress intensity factor for fracture problems). These GOEE are one of the key unsolved problems of advanced engineering applications in, for example, the aerospace industry. This work presents a simple recovery-based error estimation technique for QoIs whose main characteristic is the use of an enhanced version of the Superconvergent Patch Recovery (SPR) technique previously used for error estimation in the energy norm. This enhanced SPR technique is used to recover both the primal and dual solutions. It provides a nearly statically admissible stress field that results in accurate estimations of the local contributions to the discretisation error in the QoI and, therefore, in an accurate estimation of this magnitude. This approach leads to a technique with a reasonable computational cost that could easily be implemented into already available finite element codes, or as an independent postprocessing tool. © 2013 Springer-Verlag Berlin Heidelberg. [less ▲]

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See detailThe virtual node polygonal element method for nonlinear thermal analysis with application to hybrid laser welding
Wu, SC; Peng, X; Zhang, WH et al

in International Journal of Heat and Mass Transfer (2013), 67

The nonlinear heat transfer process occurring during hybrid laser welding was simulated using the Virtual-node Polygonal Element (VPE) method within the framework of the Finite Element Method (FEM). To ... [more ▼]

The nonlinear heat transfer process occurring during hybrid laser welding was simulated using the Virtual-node Polygonal Element (VPE) method within the framework of the Finite Element Method (FEM). To achieve robustness in large-scale welding simulations, a dynamic mesh refinement with quadtree and octree data structures was used in the welding region. Accuracy, convergence and efficiency were verified by solving two and three dimensional problems. It is found that the present VPE can successfully simulate the hybrid laser welding process with good accuracy and convergence. The adaptive refined mesh box can synchronously move with the welding heat source, which dramatically reduces the number of field nodes. Compared with the standard FEM,the VPEM requires only approximately 42% of the total degrees of freedom used in standard FEM for the same accuracy. Furthermore, we compare the computational cost and accuracy of the method to that of the finite element method, the edge based virtual node polygonal element/virtual node method, the edge-based Smoothed Point Interpolation Meshless Method (ES-PIM), the edge-based Element (ES-PIM) the Element Free Galerkin (EFG) method and the Meshless Local Petrove-Galerkin Petrov-Galerkin (MLPG) method. Compared to all those methods, the proposed scheme is found competitive in terms of computational cost versus accuracy, and benefit from a simple implementation. © 2012 Elsevier B.V. All rights reserved. [less ▲]

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See detailExtended space-time finite elements for landslide dynamics
Pasenow, F.; Zilian, Andreas UL; Dinkler, D.

in International Journal for Numerical Methods in Engineering (2013), 93(3), 329-354

The paper introduces a methodology for numerical simulation of landslides experiencing considerable deformations and topological changes. Within an interface capturing approach, all interfaces are ... [more ▼]

The paper introduces a methodology for numerical simulation of landslides experiencing considerable deformations and topological changes. Within an interface capturing approach, all interfaces are implicitly described by specifically defined level-set functions allowing arbitrarily evolving complex topologies. The transient interface evolution is obtained by solving the level-set equation driven by the physical velocity field for all three level-set functions in a block Jacobi approach. The three boundary-coupled fluid-like continua involved are modeled as incompressible, governed by a generalized non-Newtonian material law taking into account capillary pressure at moving fluid-fluid interfaces. The weighted residual formulation of the level-set equations and the fluid equations is discretized with finite elements in space and time using velocity and pressure as unknown variables. Non-smooth solution characteristics are represented by enriched approximations to fluid velocity (weak discontinuity) and fluid pressure (strong discontinuity). Special attention is given to the construction of enriched approximations for elements containing evolving triple junctions. Numerical examples of three-fluid tank sloshing and air-water-liquefied soil landslides demonstrate the potential and applicability of the method in geotechnical investigations. © 2012 John Wiley & Sons, Ltd. [less ▲]

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See detailManagement of product characteristics uncertainty based on Formal Logic and Characteristics Properties Model
Dantan, Jean-Yves; Qureshi, Ahmed Jawad UL; Antoine, J. et al

in CIRP Annals - Manufacturing Technology (2013), 62(1),

Uncertainty in product characteristics is ubiquitous in any engineering system at all the stages of product life-cycle. Considering uncertainty from different sources during the product design phase is ... [more ▼]

Uncertainty in product characteristics is ubiquitous in any engineering system at all the stages of product life-cycle. Considering uncertainty from different sources during the product design phase is critical to its reliable performance. This paper presents a framework integrating the uncertainty propagation through different product characteristics and its effect on product properties. The framework consists of three main parts: a descriptive model based on formal logic and characteristics properties model; a mathematical implementation through set theory and probabilistic approach; and an algorithm for design space evaluation and tolerancing. The application of framework is demonstrated through an industrial case study. [less ▲]

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See detailAn Analysis of Functional Modelling Approaches Across Disicplines
Eisenbart, Boris UL; Gericke, Kilian UL; Blessing, Lucienne UL

in AI EDAM: Artificial Intelligence for Engineering Design Analysis and Manufacturing (2013), 27(3),

Authors across disciplines propose functional modeling as part of systematic design approaches, in order to support and guide designers during conceptual design. The presented research aims at ... [more ▼]

Authors across disciplines propose functional modeling as part of systematic design approaches, in order to support and guide designers during conceptual design. The presented research aims at contributing to a better understanding of the diverse functional modeling approaches proposed across disciplines. The article presents a literature review of 41 modeling approaches from a variety of disciplines. The analysis focuses on what is addressed by functional modeling at which point in the proposed conceptual design process (i.e., in which sequence). The gained insights lead to the identification of specific needs and opportunities, which could support the development of an integrated functional modeling approach. The findings suggest that there is no such shared sequence for functional modeling across disciplines. However, a shared functional modeling perspective has been identified across all reviewed disciplines, which could serve as a common basis for the development of an integrated functional modeling approach. [less ▲]

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See detailSecure and Reliable Clustering in Wireless Sensor Networks: A Critical Survey
Schaffer, Peter UL; Farkas, Károly; Horváth, Ádám et al

in Computer Networks (2012), 56(11), 27262741

In the past few years, research interest has been increased towards wireless sensor networks (WSNs) and their application in both the military and civil domains. To support scalability in WSNs and ... [more ▼]

In the past few years, research interest has been increased towards wireless sensor networks (WSNs) and their application in both the military and civil domains. To support scalability in WSNs and increase network lifetime, nodes are often grouped into disjoint clusters. However, secure and reliable clustering, which is critical in WSNs deployed in hostile environments, has gained modest attention so far or has been limited only to fault tolerance. In this paper, we review the state-of-the-art of clustering protocols in WSNs with special emphasis on security and reliability issues. First, we define a taxonomy of security and reliability for cluster head election and clustering in WSNs. Then, we describe and analyze the most relevant secure and reliable clustering protocols. Finally, we propose countermeasures against typical attacks and show how they improve the discussed protocols. [less ▲]

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See detailGraphviz e TikZ
Fiandrino, Claudio UL

in Ars TeXnica (2012), 13

Graphviz is a very powerful tool to draw graphs. This article tries to explain how to export such graphs as a TikZ picture in a very simple way.

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See detailEARLY FLOWERING4 Recruitment of EARLY FLOWERING3 in the Nucleus Sustains the Arabidopsis Circadian Clock
Herrero, Eva; Kolmos, Elsebeth; Bujdoso, Nora et al

in Plant Cell (2012), 24(2), 428-443

The plant circadian clock is proposed to be a network of several interconnected feedback loops, and loss of any component leads to changes in oscillator speed. We previously reported that Arabidopsis ... [more ▼]

The plant circadian clock is proposed to be a network of several interconnected feedback loops, and loss of any component leads to changes in oscillator speed. We previously reported that Arabidopsis thaliana EARLY FLOWERING4 (ELF4) is required to sustain this oscillator and that the elf4 mutant is arrhythmic. This phenotype is shared with both elf3 and lux. Here, we show that overexpression of either ELF3 or LUX ARRHYTHMO (LUX) complements the elf4 mutant phenotype. Furthermore, ELF4 causes ELF3 to form foci in the nucleus. We used expression data to direct a mathematical position of ELF3 in the clock network. This revealed direct effects on the morning clock gene PRR9, and we determined association of ELF3 to a conserved region of the PRR9 promoter. A cis-element in this region was suggestive of ELF3 recruitment by the transcription factor LUX, consistent with both ELF3 and LUX acting genetically downstream of ELF4. Taken together, using integrated approaches, we identified ELF4/ELF3 together with LUX to be pivotal for sustenance of plant circadian rhythms. [less ▲]

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See detailGlobal State Synchronization in Networks of Cyclic Feedback Systems
Hamadeh, Abdullah; Stan, Guy-Bart; Sepulchre, Rodolphe et al

in IEEE Transactions on Automatic Control (2012), 57(2), 478-483

This technical note studies global asymptotic state synchronization in networks of identical systems. Conditions on the coupling strength required for the synchronization of nodes having a cyclic feedback ... [more ▼]

This technical note studies global asymptotic state synchronization in networks of identical systems. Conditions on the coupling strength required for the synchronization of nodes having a cyclic feedback structure are deduced using incremental dissipativity theory. The method takes advantage of the incremental passivity properties of the constituent subsystems of the network nodes to reformulate the synchronization problem as one of achieving incremental passivity by coupling. The method can be used in the framework of contraction theory to constructively build a contracting metric for the incremental system. The result is illustrated for a network of biochemical oscillators. [less ▲]

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See detailExploiting Resource Heterogeneity in DTN
Sandulescu, Gabriel UL; Schaffer, Peter UL; Nadjm-Tehrani, Simin UL

in Wireless Communications & Mobile Computing (2012), 13(3), 230-243

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See detailOn the role of enrichment and statistical admissibility of recovered fields in a posteriori error estimation for enriched finite element methods
González-Estrada, O. A.; Ródenas, J. J.; Bordas, Stéphane UL et al

in Engineering Computations (2012), 29(8), 814-841

Purpose - The purpose of this paper is to assess the effect of the statistical admissibility of the recovered solution and the ability of the recovered solution to represent the singular solution; also ... [more ▼]

Purpose - The purpose of this paper is to assess the effect of the statistical admissibility of the recovered solution and the ability of the recovered solution to represent the singular solution; also the accuracy, local and global effectivity of recovery-based error estimators for enriched finite element methods (e.g. the extended finite element method, XFEM). Design/methodology/approach - The authors study the performance of two recovery techniques. The first is a recently developed superconvergent patch recovery procedure with equilibration and enrichment (SPR-CX). The second is known as the extended moving least squares recovery (XMLS), which enriches the recovered solutions but does not enforce equilibrium constraints. Both are extended recovery techniques as the polynomial basis used in the recovery process is enriched with singular terms for a better description of the singular nature of the solution. Findings - Numerical results comparing the convergence and the effectivity index of both techniques with those obtained without the enrichment enhancement clearly show the need for the use of extended recovery techniques in Zienkiewicz-Zhu type error estimators for this class of problems. The results also reveal significant improvements in the effectivities yielded by statistically admissible recovered solutions. Originality/value - The paper shows that both extended recovery procedures and statistical admissibility are key to an accurate assessment of the quality of enriched finite element approximations. © Emerald Group Publishing Limited. [less ▲]

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See detailExtended finite element method for dynamic fracture of piezo-electric materials
Nguyen-Vinh, H.; Bakar, I.; Msekh, M. A. et al

in Engineering Fracture Mechanics (2012), 92

We present an extended finite element formulation for dynamic fracture of piezo-electric materials. The method is developed in the context of linear elastic fracture mechanics. It is applied to mode I and ... [more ▼]

We present an extended finite element formulation for dynamic fracture of piezo-electric materials. The method is developed in the context of linear elastic fracture mechanics. It is applied to mode I and mixed mode-fracture for quasi-steady cracks. An implicit time integration scheme is exploited. The results are compared to results obtained with the boundary element method and show excellent agreement. [less ▲]

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See detailA cell-based smoothed finite element method for three dimensional solid structures
Nguyen-Xuan, Hung; Nguyen, Ha Manh UL; Bordas, Stéphane UL et al

in KSCE Journal of Civil Engineering (2012), 16(7), 1230-1242

This paper extends further the strain smoothing technique in finite elements to 8-noded hexahedral elements (CS-FEM-H8). The idea behind the present method is similar to the cell-based smoothed 4-noded ... [more ▼]

This paper extends further the strain smoothing technique in finite elements to 8-noded hexahedral elements (CS-FEM-H8). The idea behind the present method is similar to the cell-based smoothed 4-noded quadrilateral finite elements (CS-FEM-Q4). In CSFEM, the smoothing domains are created based on elements, and each element can be further subdivided into 1 or several smoothing cells. It is observed that: 1) The CS-FEM using a single smoothing cell can produce higher stress accuracy, but insufficient rank and poor displacement accuracy; 2) The CS-FEM using several smoothing cells has proper rank, good displacement accuracy, but lower stress accuracy, especially for nearly incompressible and bending dominant problems. We therefore propose 1) an extension of strain smoothing to 8-noded hexahedral elements and 2) an alternative CS-FEM form, which associates the single smoothing cell issue with multi-smoothing cell one via a stabilization technique. Several numerical examples are provided to show the reliability and accuracy of the present formulation. [less ▲]

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See detailA locking-free meshfree method for the simulation of shear-deformable plates based on a mixed variational formulation
Hale, Jack UL; Baiz, P. M.

in Computer Methods in Applied Mechanics and Engineering (2012), 241-244

The problem of shear-locking in the thin-plate limit is a well known issue that must be overcome when discretising the Reissner-Mindlin plate equations. In this paper we present a shear-locking-free ... [more ▼]

The problem of shear-locking in the thin-plate limit is a well known issue that must be overcome when discretising the Reissner-Mindlin plate equations. In this paper we present a shear-locking-free method utilising meshfree maximum-entropy basis functions and rotated Raviart-Thomas-Nédélec elements within a mixed variational formulation. The formulation draws upon well known techniques in the finite element literature. Due to the inherent properties of the maximum-entropy basis functions our method allows for the direct imposition of Dirichlet (essential) boundary conditions, in contrast to methods based on moving least squares basis functions. We present benchmark problems that demonstrate the accuracy and performance of the proposed method. © 2012. [less ▲]

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See detailA Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel
Czeizler, Elena; Mizera, Andrzej UL; Petre, Ion

in Fundamenta Informaticae (2012), 116(1-4), 51-63

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See detailQuantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction
Haraldsdottir, Hulda UL; Thiele, Ines UL; Fleming, Ronan MT UL

in Biophysical Journal (2012), 102(8), 17031711

Reaction directionality is a key constraint in the modeling of genome-scale metabolic networks. We thermodynamically constrained reaction directionality in a multicompartmental genome-scale model of human ... [more ▼]

Reaction directionality is a key constraint in the modeling of genome-scale metabolic networks. We thermodynamically constrained reaction directionality in a multicompartmental genome-scale model of human metabolism, Recon 1, by calculating, in vivo, standard transformed reaction Gibbs energy as a function of compartment-specific pH, electrical potential, and ionic strength. We show that compartmental pH is an important determinant of thermodynamically determined reaction directionality. The effects of pH on transport reaction thermodynamics are only seen to their full extent when metabolites are represented as pseudoisomer groups of multiple protonated species. We accurately predict the irreversibility of 387 reactions, with detailed propagation of uncertainty in input data, and manually curate the literature to resolve conflicting directionality assignments. In at least half of all cases, a prediction of a reversible reaction directionality is due to the paucity of compartment-specific quantitative metabolomic data, with remaining cases due to uncertainty in estimation of standard reaction Gibbs energy. This study points to the pressing need for 1), quantitative metabolomic data, and 2), experimental measurement of thermochemical properties for human metabolites. [less ▲]

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See detailDigital (r) evolution in private customer business \ "a ft? Call to banks to act proactively
Buhl, Hans Ulrich; Eistert, Torsten; Fridgen, Gilbert UL et al

in Die Bank (2012), 52(6), 46--50

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See detailA two-dimensional Isogeometric Boundary Element Method for elastostatic analysis
Simpson, R. N.; Bordas, Stéphane UL; Trevelyan, J. et al

in Computer Methods in Applied Mechanics and Engineering (2012), 209-212

The concept of isogeometric analysis, where functions that are used to describe geometry in CAD software are used to approximate the unknown fields in numerical simulations, has received great attention ... [more ▼]

The concept of isogeometric analysis, where functions that are used to describe geometry in CAD software are used to approximate the unknown fields in numerical simulations, has received great attention in recent years. The method has the potential to have profound impact on engineering design, since the task of meshing, which in some cases can add significant overhead, has been circumvented. Much of the research effort has been focused on finite element implementations of the isogeometric concept, but at present, little has been seen on the application to the Boundary Element Method. The current paper proposes an Isogeometric Boundary Element Method (BEM), which we term IGABEM, applied to two-dimensional elastostatic problems using Non-Uniform Rational B-Splines (NURBS). We find it is a natural fit with the isogeometric concept since both the NURBS approximation and BEM deal with quantities entirely on the boundary. The method is verified against analytical solutions where it is seen that superior accuracies are achieved over a conventional quadratic isoparametric BEM implementation. © 2011 Elsevier B.V. [less ▲]

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See detailEnriched residual free bubbles for semiconductor device simulation
Simpson, R. N.; Bordas, Stéphane UL; Asenov, A. et al

in Computational Mechanics (2012), 50(1), 119-133

This article outlines a method for stabilising the current continuity equations which are used for semiconductor device simulation. Residual-free bubble functions (RfBF) are incorporated into a finite ... [more ▼]

This article outlines a method for stabilising the current continuity equations which are used for semiconductor device simulation. Residual-free bubble functions (RfBF) are incorporated into a finite element (FE) implementation that are able to prevent oscillations which are seen when using the conventional Bubnov-Galerkin FE implementation. In addition, it is shown that the RfBF are able to provide stabilisation with very distorted meshes and curved interface boundaries. Comparison with the commonly used SUPG scheme is made throughout, showing that in the case of 2D problems the RfBF allow faster convergence of the coupled semiconductor device equations, especially in the case of distorted meshes. [less ▲]

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See detailLocal/global model order reduction strategy for the simulation of quasi-brittle fracture
Kerfriden, P.; Passieux, J. C.; Bordas, Stéphane UL

in International Journal for Numerical Methods in Engineering (2012), 89(2), 154-179

This paper proposes a novel technique to reduce the computational burden associated with the simulation of localized failure. The proposed methodology affords the simulation of damage initiation and ... [more ▼]

This paper proposes a novel technique to reduce the computational burden associated with the simulation of localized failure. The proposed methodology affords the simulation of damage initiation and propagation while concentrating the computational effort where it is most needed, that is, in the localization zones. To do so, a local/global technique is devised where the global (slave) problem (far from the zones undergoing severe damage and cracking) is solved for in a reduced space computed by the classical proper orthogonal decomposition while the local (master) degrees of freedom (associated with the part of the structure where most of the damage is taking place) are fully resolved. Both domains are coupled through a local/global technique. This method circumvents the difficulties associated with model order reduction for the simulation of highly nonlinear mechanical failure and offers an alternative or complementary approach to the development of multiscale fracture simulators. © 2011 John Wiley & Sons, Ltd. [less ▲]

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See detailRecent developments in CAD/analysis integration
Lian, Haojie; Bordas, Stéphane UL; Sevilla, Rubén

in Computational Technology Reviews (2012), 6

For linear elastic problems, it is well-known that mesh generation dominates the total analysis time. Different types of methods have been proposed to directly or indirectly alleviate this burden ... [more ▼]

For linear elastic problems, it is well-known that mesh generation dominates the total analysis time. Different types of methods have been proposed to directly or indirectly alleviate this burden associated with mesh generation. We review in this paper a subset of such methods centred on tighter coupling between computer aided design (CAD) and analysis (finite element or boundary element methods). We focus specifically on frameworks which rely on constructing a discretisation directly from the functions used to describe the geometry of the object in CAD. Examples include B-spline subdivision surfaces, isogeometric analysis, NURBS-enhanced FEM and parametric-based implicit boundary definitions. We review recent advances in these methods and compare them to other paradigms which also aim at alleviating the burden of mesh generation in computational mechanics. [less ▲]

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See detailExtended finite element method with edge-based strain smoothing (ESm-XFEM) for linear elastic crack growth
Chen, L.; Rabczuk, T.; Bordas, Stéphane UL et al

in Computer Methods in Applied Mechanics and Engineering (2012), 209-212

This paper presents a strain smoothing procedure for the extended finite element method (XFEM). The resulting "edge-based" smoothed extended finite element method (ESm-XFEM) is tailored to linear elastic ... [more ▼]

This paper presents a strain smoothing procedure for the extended finite element method (XFEM). The resulting "edge-based" smoothed extended finite element method (ESm-XFEM) is tailored to linear elastic fracture mechanics and, in this context, to outperform the standard XFEM. In the XFEM, the displacement-based approximation is enriched by the Heaviside and asymptotic crack tip functions using the framework of partition of unity. This eliminates the need for the mesh alignment with the crack and re-meshing, as the crack evolves. Edge-based smoothing (ES) relies on a generalized smoothing operation over smoothing domains associated with edges of simplex meshes, and produces a softening effect leading to a close-to-exact stiffness, "super-convergence" and "ultra-accurate" solutions. The present method takes advantage of both the ES-FEM and the XFEM. Thanks to the use of strain smoothing, the subdivision of elements intersected by discontinuities and of integrating the (singular) derivatives of the approximation functions is suppressed via transforming interior integration into boundary integration. Numerical examples show that the proposed method improves significantly the accuracy of stress intensity factors and achieves a near optimal convergence rate in the energy norm even without geometrical enrichment or blending correction. [less ▲]

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See detailA mixed integer linear programming approach to pursuit evasion problems with optional connectivity constraints
Thunberg, Johan UL; Ögren, P.

in Autonomous Robots (2011), 31(4), 333-343

In this paper, we address the multi pursuer version of the pursuit evasion problem in polygonal environments. By discretizing the problem, and applying a Mixed Integer Linear Programming (MILP) framework ... [more ▼]

In this paper, we address the multi pursuer version of the pursuit evasion problem in polygonal environments. By discretizing the problem, and applying a Mixed Integer Linear Programming (MILP) framework, we are able to address problems requiring so-called recontamination and also impose additional constraints, such as connectivity between the pursuers. The proposed MILP formulation is less conservative than solutions based on graph discretizations of the environment, but still somewhat more conservative than the original underlying problem. It is well known that MILPs, as well as multi pursuer pursuit evasion problems, are NP-hard. Therefore we apply an iterative Receding Horizon Control (RHC) scheme where a number of smaller MILPs are solved over shorter planning horizons. The proposed approach is implemented in Matlab/Cplex and illustrated by a number of solved examples. [less ▲]

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See detailRobust dynamical network structure reconstruction
Yuan, Ye; Stan, Guy-Bart; Warnick, Stan et al

in Automatica (2011), 47(6),

This paper addresses the problem of network reconstruction from data. Previous work identified necessary and sufficient conditions for network reconstruction of LTI systems, assuming perfect measurements ... [more ▼]

This paper addresses the problem of network reconstruction from data. Previous work identified necessary and sufficient conditions for network reconstruction of LTI systems, assuming perfect measurements (no noise) and perfect system identification. This paper assumes that the conditions for network reconstruction have been met but here we additionally take into account noise and unmodelled dynamics (including nonlinearities). In order to identify the network structure that generated the data, we compute the smallest distances between the measured data and the data that would have been generated by particular network structures. We conclude with biologically inspired network reconstruction examples which include noise and nonlinearities. [less ▲]

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See detailThe circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose
Dalchau, Neil; Baek, Seong; Briggs, Helen et al

in PNAS (2011), 108(12), 51045109

Circadian clocks are 24-h timing devices that phase cellular responses; coordinate growth, physiology, and metabolism; and anticipate the day–night cycle. Here we report sensitivity of the Arabidopsis ... [more ▼]

Circadian clocks are 24-h timing devices that phase cellular responses; coordinate growth, physiology, and metabolism; and anticipate the day–night cycle. Here we report sensitivity of the Arabidopsis thaliana circadian oscillator to sucrose, providing evidence that plant metabolism can regulate circadian function. We found that the Arabidopsis circadian system is particularly sensitive to sucrose in the dark. These data suggest that there is a feedback between the molecular components that comprise the circadian oscillator and plant metabolism, with the circadian clock both regulating and being regulated by metabolism. We used also simulations within a three-loop mathematical model of the Arabidopsis circadian oscillator to identify components of the circadian clock sensitive to sucrose. The mathematical studies identified GIGANTEA (GI) as being associatedwith sucrose sensing. Experimental validation of this prediction demonstrated that GI is required for the full response of the circadian clock to sucrose. We demonstrate that GI acts as part of the sucrose-signaling network and propose this role permits metabolic input into circadian timing in Arabidopsis. [less ▲]

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See detailOn Judgment Aggregation in Abstract Argumentation
Caminada, Martin UL; Pigozzi, Gabriella UL

in Autonomous Agents & Multi-Agent Systems (2011), 22(1), 64102

Judgment aggregation is a field in which individuals are required to vote for or against a certain decision (the conclusion) while providing reasons for their choice. The reasons and the conclusion are ... [more ▼]

Judgment aggregation is a field in which individuals are required to vote for or against a certain decision (the conclusion) while providing reasons for their choice. The reasons and the conclusion are logically connected propositions. The problem is how a collective judgment on logically interconnected propositions can be defined from individual judgments on the same propositions. It turns out that, despite the fact that the individuals are logically consistent, the aggregation of their judgments may lead to an inconsistent group outcome, where the reasons do not support the conclusion. However, in this paper we claim that collective irrationality should not be the only worry of judgment aggregation. For example, judgment aggregation would not reject a consistent combination of reasons and conclusion that no member voted for. In our view this may not be a desirable solution. This motivates our research about when a social outcome is ‘compatible’ with the individuals’ judgments. The key notion that we want to capture is that any individual member has to be able to defend the collective decision. This is guaranteed when the group outcome is compatible with its members views. Judgment aggregation problems are usually studied using classical propositional logic. However, for our analysis we use an argumentation approach to judgment aggregation problems. Indeed the question of how individual evaluations can be combined into a collective one can also be addressed in abstract argumentation. We introduce three aggregation operators that satisfy the condition above, and we offer two definitions of compatibility. Not only does our proposal satisfy a good number of standard judgment aggregation postulates, but it also avoids the problem of individual members of a group having to become committed to a group judgment that is in conflict with their own individual positions. [less ▲]

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See detailAccurate fracture modelling using meshless methods, the visibility criterion and level sets: Formulation and 2D modelling
Zhuang, Xiaoying; Augarde, Charles; Bordas, Stéphane UL

in International Journal for Numerical Methods in Engineering (2011), 86(2), 249-268

Fracture modelling using numerical methods is well-advanced in 2D using techniques such as the extended finite element method (XFEM). The use of meshless methods for these problems lags somewhat behind ... [more ▼]

Fracture modelling using numerical methods is well-advanced in 2D using techniques such as the extended finite element method (XFEM). The use of meshless methods for these problems lags somewhat behind, but the potential benefits of no meshing (particularly in 3D) prompt continued research into their development. In methods where the crack face is not explicitly modelled (as the edge of an element for instance), two procedures are instead used to associate the displacement jump with the crack surface: the visibility criterion and the diffraction method. The visibility criterion is simple to implement and efficient to compute, especially with the help of level set coordinates. However, spurious discontinuities have been reported around crack tips using the visibility criterion, whereas implementing the diffraction method in 3D is much more complicated than the visibility criterion. In this paper, a tying procedure is proposed to remove the difficulty with the visibility criterion so that crack tip closure can be ensured while the advantages of the visibility criterion can be preserved. The formulation is based on the use of level set coordinates and the element-free Galerkin method, and is generally applicable for single or multiple crack problems in 2D or 3D. The paper explains the formulation and provides verification of the method against a number of 2D crack problems. [less ▲]

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See detailA simple mass-action model for the eukaryotic heat shock response and its mathematical validation
Petre, Ion; Mizera, Andrzej UL; Hyder, Claire L. et al

in Natural Computing (2011), 10(1), 595-612

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See detailLocalized meshless point collocation method for time-dependent magnetohydrodynamics flow through pipes under a variety of wall conductivity conditions
Loukopoulos, Vasilis; Bourantas, Georgios UL; Skouras, Eugene

in Computational Mechanics (2011), 47(2), 137-159

In this article a numerical solution of the time dependent, coupled system equations of magnetohydrody- namics (MHD) flow is obtained, using the strong-form local meshless point collocation (LMPC) method ... [more ▼]

In this article a numerical solution of the time dependent, coupled system equations of magnetohydrody- namics (MHD) flow is obtained, using the strong-form local meshless point collocation (LMPC) method. The approxima- tion of the field variables is obtained with the moving least squares (MLS) approximation. Regular and irregular nodal distributions are used. Thus, a numerical solver is developed for the unsteady coupled MHD problems, using the collo- cation formulation, for regular and irregular cross sections, as are the rectangular, triangular and circular. Arbitrary wall conductivity conditions are applied when a uniform mag- netic field is imposed at characteristic directions relative to the flow one. Velocity and induced magnetic field across the section have been evaluated at various time intervals for sev- eral Hartmann numbers (up to 105) and wall conductivities. The numerical results of the strong-form MPC method are compared with those obtained using two weak-form mesh- less methods, that is, the local boundary integral equation (LBIE) meshless method and the meshless local Petrov– Galerkin (MLPG) method, and with the analytical solutions, where they are available. Furthermore, the accuracy of the method is assessed in terms of the error norms L 2 and L ∞ , the number of nodes in the domain of influence and the time step length depicting the convergence rate of the method. Run time results are also presented demonstrating the efficiency and the applicability of the method for real world problems. [less ▲]

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See detailMethods for Biochemical Model Decomposition and Quantitative Submodel Comparison
Mizera, Andrzej UL; Czeizler, Elena; Petre, Ion

in Israel Journal of Chemistry (2011), 51(1), 151164

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See detailRobust stability of delayed genetic regulatory networks with different sources of uncertainties
Pan, Wei UL; Wang, Z.; Hu, J.

in Asian Journal of Control (2011), 13(5), 645-654

Gene regulation is inherently a stochastic process due to intrinsic and extrinsic noises which cause the fluctuations and uncertainties of kinetic parameters. On the other hand, time delays are usually ... [more ▼]

Gene regulation is inherently a stochastic process due to intrinsic and extrinsic noises which cause the fluctuations and uncertainties of kinetic parameters. On the other hand, time delays are usually inevitable due to different biochemical reactions in the genetic regulatory networks (GRNs) which are also affected by noises. Therefore, in this paper, we propose a GRN model that is subject to additive and multiplicative noises as well as time-varying delays. The time-varying delay is assumed to belong to an interval and no restriction on the derivative of the time-varying delay is needed, which allows the delay to be a fast time-varying function. Robust stochastic stability of such GRNs with disturbance attenuation is analyzed by applying the control theory and mathematical tools. Based on the Lyapunov method, new stability conditions are derived in the form of linear matrix inequalities that are dependent on the upper and lower bounds of time delays. An example is employed to illustrate the applicability and usefulness of the developed theoretical results. [less ▲]

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See detailA node-based smoothed extended finite element method (NS-XFEM) for fracture analysis
Vu-Bac, N.; Nguyen-Xuan, H.; Chen, L. et al

in Computer Modeling in Engineering and Sciences (2011), 73(4), 331-355

This paper aims to incorporate the node-based smoothed finite element method (NS-FEM) into the extended finite element method (XFEM) to form a novel numerical method (NS-XFEM) for analyzing fracture ... [more ▼]

This paper aims to incorporate the node-based smoothed finite element method (NS-FEM) into the extended finite element method (XFEM) to form a novel numerical method (NS-XFEM) for analyzing fracture problems of 2D elasticity. NS-FEM uses the strain smoothing technique over the smoothing domains associated with nodes to compute the system stiffness matrix, which leads to the line integrations using directly the shape function values along the boundaries of the smoothing domains. As a result, we avoid integration of the stress singularity at the crack tip. It is not necessary to divide elements cut by cracks when we replace interior integration by boundary integration, simplifying integration of the discontinuous approximation. The key advantage of the NS-XFEM is that it provides more accurate solutions compared to the XFEM-T3 element. We will show for two numerical examples that the NS-XFEM significantly improves the results in the energy norm and the stress intensity factors. For the examples studied, we obtain super-convergent results. [less ▲]

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See detailFinite element analysis on implicitly defined domains: An accurate representation based on arbitrary parametric surfaces
Moumnassi, M.; Belouettar, S.; Béchet, T. et al

in Computer Methods in Applied Mechanics and Engineering (2011), 200(5-8), 774-796

In this paper, we present some novel results and ideas for robust and accurate implicit representation of geometric surfaces in finite element analysis. The novel contributions of this paper are threefold ... [more ▼]

In this paper, we present some novel results and ideas for robust and accurate implicit representation of geometric surfaces in finite element analysis. The novel contributions of this paper are threefold: (1) describe and validate a method to represent arbitrary parametric surfaces implicitly; (2) represent arbitrary solids implicitly, including sharp features using level sets and boolean operations; (3) impose arbitrary Dirichlet and Neumann boundary conditions on the resulting implicitly defined boundaries. The methods proposed do not require local refinement of the finite element mesh in regions of high curvature, ensure the independence of the domain's volume on the mesh, do not rely on boundary regularization, and are well suited to methods based on fixed grids such as the extended finite element method (XFEM). Numerical examples are presented to demonstrate the robustness and effectiveness of the proposed approach and show that it is possible to achieve optimal convergence rates using a fully implicit representation of object boundaries. This approach is one step in the desired direction of tying numerical simulations to computer aided design (CAD), similarly to the isogeometric analysis paradigm. © 2010 Elsevier B.V. [less ▲]

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See detailUnderstanding dynamics using sensitivity analysis: caveat and solution
Perumal, Thanneer Malai UL; Gunawan, Rudiyanto

in BMC Systems Biology (2011), 5

BACKGROUND: Parametric sensitivity analysis (PSA) has become one of the most commonly used tools in computational systems biology, in which the sensitivity coefficients are used to study the parametric ... [more ▼]

BACKGROUND: Parametric sensitivity analysis (PSA) has become one of the most commonly used tools in computational systems biology, in which the sensitivity coefficients are used to study the parametric dependence of biological models. As many of these models describe dynamical behaviour of biological systems, the PSA has subsequently been used to elucidate important cellular processes that regulate this dynamics. However, in this paper, we show that the PSA coefficients are not suitable in inferring the mechanisms by which dynamical behaviour arises and in fact it can even lead to incorrect conclusions. RESULTS: A careful interpretation of parametric perturbations used in the PSA is presented here to explain the issue of using this analysis in inferring dynamics. In short, the PSA coefficients quantify the integrated change in the system behaviour due to persistent parametric perturbations, and thus the dynamical information of when a parameter perturbation matters is lost. To get around this issue, we present a new sensitivity analysis based on impulse perturbations on system parameters, which is named impulse parametric sensitivity analysis (iPSA). The inability of PSA and the efficacy of iPSA in revealing mechanistic information of a dynamical system are illustrated using two examples involving switch activation. CONCLUSIONS: The interpretation of the PSA coefficients of dynamical systems should take into account the persistent nature of parametric perturbations involved in the derivation of this analysis. The application of PSA to identify the controlling mechanism of dynamical behaviour can be misleading. By using impulse perturbations, introduced at different times, the iPSA provides the necessary information to understand how dynamics is achieved, i.e. which parameters are essential and when they become important. [less ▲]

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See detailA cell - based smoothed finite element method for free vibration and buckling analysis of shells
Thai-Hoang, Chien; Nguyen-Thanh, Nhon; Nguyen-Xuan, Hung et al

in KSCE Journal of Civil Engineering (2011), 15(2), 347-361

This paper further extends a cell-based smoothed finite element method for free vibration and buckling analysis of shells. A four-node quadrilateral Mindlin-Reissner shell element with a gradient ... [more ▼]

This paper further extends a cell-based smoothed finite element method for free vibration and buckling analysis of shells. A four-node quadrilateral Mindlin-Reissner shell element with a gradient smoothing operator is adopted. The membrane-bending and geometrical stiffness matrices are computed along the boundaries of the smoothing cells while the shear stiffness matrix is calculated by an independent interpolation in the natural coordinates as in the MITC4 (the Mixed Interpolation of Tensorial Components) element. Various numerical results are compared with existing exact and numerical solutions and they are in good agreement. The advantage of the present formulation is that it retains higher accurate than the MITC4 element even for heavily distorted meshes without increasing the computational cost. © 2011 Korean Society of Civil Engineers and Springer-Verlag Berlin Heidelberg. [less ▲]

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See detailIsogeometric analysis using polynomial splines over hierarchical T-meshes for two-dimensional elastic solids
Nguyen-Thanh, N.; Nguyen-Xuan, H.; Bordas, Stéphane UL et al

in Computer Methods in Applied Mechanics and Engineering (2011), 200(21-22), 1892-1908

Isogeometric analysis has become a powerful alternative to standard finite elements due to its flexibility in handling complex geometries. One of the major drawbacks of NURBS-based isogeometric finite ... [more ▼]

Isogeometric analysis has become a powerful alternative to standard finite elements due to its flexibility in handling complex geometries. One of the major drawbacks of NURBS-based isogeometric finite elements is the inefficiency of local refinement. In this study, we present an alternative to NURBS-based isogeometric analysis that allows for local refinement. The idea is based on polynomial splines and exploits the flexibility of T-meshes for local refinement. The shape functions satisfy important properties such as non-negativity, local support and partition of unity. Several numerical examples are used to demonstrate the reliability of the present method. [less ▲]

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See detailA rheological interface model and its space-time finite element formulation for fluid-structure interaction
Legay, A.; Zilian, Andreas UL; Janssen, C.

in International Journal for Numerical Methods in Engineering (2011), 86(6), 667-687

This contribution discusses extended physical interface models for fluid-structure interaction problems and investigates their phenomenological effects on the behavior of coupled systems by numerical ... [more ▼]

This contribution discusses extended physical interface models for fluid-structure interaction problems and investigates their phenomenological effects on the behavior of coupled systems by numerical simulation. Besides the various types of friction at the fluid-structure interface the most interesting phenomena are related to effects due to additional interface stiffness and damping. The paper introduces extended models at the fluid-structure interface on the basis of rheological devices (Hooke, Newton, Kelvin, Maxwell, Zener). The interface is decomposed into a Lagrangian layer for the solid-like part and an Eulerian layer for the fluid-like part. The mechanical model for fluid-structure interaction is based on the equations of rigid body dynamics for the structural part and the incompressible Navier-Stokes equations for viscous flow. The resulting weighted residual form uses the interface velocity and interface tractions in both layers in addition to the field variables for fluid and structure. The weak formulation of the whole coupled system is discretized using space-time finite elements with a discontinuous Galerkin method for time-integration leading to a monolithic algebraic system. The deforming fluid domain is taken into account by deformable space-time finite elements and a pseudo-structure approach for mesh motion. The sensitivity of coupled systems to modification of the interface model and its parameters is investigated by numerical simulation of flow induced vibrations of a spring supported fluid-immersed cylinder. It is shown that the presented rheological interface model allows to influence flow-induced vibrations. © 2010 John Wiley & Sons, Ltd. [less ▲]

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See detailExtended Finite Element Method
Fries, T.-P.; Zilian, Andreas UL; Moës, N.

in International Journal for Numerical Methods in Engineering (2011), 86(4-5), 403

[No abstract available]

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See detailLinear buckling analysis of cracked plates by SFEM and XFEM
Baiz, P. M.; Natarajan, S.; Bordas, Stéphane UL et al

in Journal of Mechanics of Material and Structures (2011), 6(9-10), 1213-1238

In this paper, the linear buckling problem for isotropic plates is studied using a quadrilateral element with smoothed curvatures and the extended finite element method. First, the curvature at each point ... [more ▼]

In this paper, the linear buckling problem for isotropic plates is studied using a quadrilateral element with smoothed curvatures and the extended finite element method. First, the curvature at each point is obtained by a nonlocal approximation via a smoothing function. This element is later coupled with partition of unity enrichment to simplify the simulation of cracks. The proposed formulation suppresses locking and yields elements which behave very well, even in the thin plate limit. The buckling coefficient and mode shapes of square and rectangular plates are computed as functions of crack length, crack location, and plate thickness. The effects of different boundary conditions are also studied. © 2011 by Mathematical Sciences Publishers. [less ▲]

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See detailOn the performance of strain smoothing for quadratic and enriched finite element approximations (XFEM/GFEM/PUFEM)
Bordas, Stéphane UL; Natarajan, S.; Kerfriden, P. et al

in International Journal for Numerical Methods in Engineering (2011), 86(4-5), 637-666

By using the strain smoothing technique proposed by Chen et al. (Comput. Mech. 2000; 25:137-156) for meshless methods in the context of the finite element method (FEM), Liu et al. (Comput. Mech. 2007; 39 ... [more ▼]

By using the strain smoothing technique proposed by Chen et al. (Comput. Mech. 2000; 25:137-156) for meshless methods in the context of the finite element method (FEM), Liu et al. (Comput. Mech. 2007; 39(6):859-877) developed the Smoothed FEM (SFEM). Although the SFEM is not yet well understood mathematically, numerical experiments point to potentially useful features of this particularly simple modification of the FEM. To date, the SFEM has only been investigated for bilinear and Wachspress approximations and is limited to linear reproducing conditions. The goal of this paper is to extend the strain smoothing to higher order elements and to investigate numerically in which condition strain smoothing is beneficial to accuracy and convergence of enriched finite element approximations. We focus on three widely used enrichment schemes, namely: (a) weak discontinuities; (b) strong discontinuities; (c) near-tip linear elastic fracture mechanics functions. The main conclusion is that strain smoothing in enriched approximation is only beneficial when the enrichment functions are polynomial (cases (a) and (b)), but that non-polynomial enrichment of type (c) lead to inferior methods compared to the standard enriched FEM (e.g. XFEM). © 2011 John Wiley & Sons, Ltd. [less ▲]

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See detailAn alternative alpha finite element method with discrete shear gap technique for analysis of isotropic Mindlin-Reissner plates
Nguyen-Thanh, N.; Rabczuk, Timon; Nguyen-Xuan, H. et al

in Finite Elements in Analysis and Design (2011), 47(5), 519-535

An alternative alpha finite element method (AαFEM) coupled with a discrete shear gap technique for triangular elements is presented to significantly improve the accuracy of the standard triangular finite ... [more ▼]

An alternative alpha finite element method (AαFEM) coupled with a discrete shear gap technique for triangular elements is presented to significantly improve the accuracy of the standard triangular finite elements for static, free vibration and buckling analyses of MindlinReissner plates. In the AαFEM, the piecewise constant strain field of linear triangular elements is enhanced by additional strain terms with an adjustable parameter α which results in an effectively softer stiffness formulation compared to the linear triangular element. To avoid the transverse shear locking, the discrete shear gap technique (DSG) is utilized and a novel triangular element, the Aα-DSG3 is obtained. Several numerical examples show that the Aα-DSG3 achieves high reliability compared to other existing elements in the literature. Through selection of α, under or over estimation of the strain energy can be achieved. [less ▲]

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See detailAn Algorithm to compute damage from load in composites
Dunant, Cyrille F.; Bordas, Stéphane UL; Kerfriden, Pierre et al

in Frontiers of Architecture and Civil Engineering in China (2011), 5(2), 180-193

We present a new method to model fracture of concrete based on energy minimisation. The concrete is considered on the mesoscale as composite consisting of cement paste, aggregates and micro pores. In this ... [more ▼]

We present a new method to model fracture of concrete based on energy minimisation. The concrete is considered on the mesoscale as composite consisting of cement paste, aggregates and micro pores. In this first step, the alkali-silica reaction is taken into account through damage mechanics though the process is more complex involving thermo-hygro-chemo-mechanical reaction. We use a non-local damage model that ensures the well-posedness of the boundary value problem (BVP). In contrast to existing methods, the interactions between degrees of freedom evolve with the damage evolutions. Numerical results are compared to analytical and experimental results and show good agreement. [less ▲]

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See detailSystems approaches to modelling pathways and networks
Pfau, Thomas UL; Christian, Nils UL; Ebenhöh, Oliver

in Briefings in Functional Genomics (2011), 10(5), 266-279

It has become commonly accepted that systems approaches to biology are of outstanding importance to gain understanding from the vast amount of data which is presently being generated by advancing high ... [more ▼]

It has become commonly accepted that systems approaches to biology are of outstanding importance to gain understanding from the vast amount of data which is presently being generated by advancing high-throughput technologies. The diversity of methods to model pathways and networks has significantly expanded over the past two decades. Modern and traditional approaches are equally important and recent activities aim at integrating the advantages of both. While traditional methods, based on differential equations, are useful to study the dynamics of small systems, modern constraint-based models can be applied to genome-scale systems, but are not able to capture dynamic features. Integrating different approaches is important to develop consistent theoretical descriptions encompassing various scales of biological information. The rapid progress of the field of theoretical systems biology, however, demonstrates how our fundamental theoretical understanding of biology is gaining momentum. The scientific community has apparently accepted the challenge to truly understand the principles of life. [less ▲]

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See detailCrack growth calculations in solder joints based on microstructural phenomena with X-FEM
Menk, Alexander; Bordas, Stéphane UL

in Computational Materials Science (2011), 50(3), 1145-1156

Determining the lifetime of solder joints subjected to thermomechanical loads is crucial to guarantee the quality of electronic devices. The fatigue process is heavily dependent on the microstructure of ... [more ▼]

Determining the lifetime of solder joints subjected to thermomechanical loads is crucial to guarantee the quality of electronic devices. The fatigue process is heavily dependent on the microstructure of the joints. We present a new methodology to determine the lifetime of the joints based on microstructural phenomena. Random microstructures are generated to capture the statistical variety of possible microstructures and crack growth calculations are performed. The extended finite element method is used to solve the structural problem numerically which allows a complete automation of the process. Numerical examples are given and compared to experimental data. [less ▲]

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See detailModelling of ultrasound therapeutic heating and numerical study of the dynamics of the induced heat shock response
Mizera, Andrzej UL; Gambin, Barbara

in Communications in Nonlinear Science and Numerical Simulation (2011), 16(5), 23422349

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See detailAn adaptive high-gain observer for nonlinear systems
Boizot, Nicolas UL; Busvelle, Eric; Gauthier, Jean-Paul

in Automatica (2010), 46(9), 1483-1488

In this paper the authors provide a solution to the noise sensitivity of high-gain observers. The resulting nonlinear observer possesses simultaneously 1) extended Kalman filter's good noise filtering ... [more ▼]

In this paper the authors provide a solution to the noise sensitivity of high-gain observers. The resulting nonlinear observer possesses simultaneously 1) extended Kalman filter's good noise filtering properties, and 2) the reactivity of the high-gain extended Kalman filter with respect to large perturbations. The authors introduce innovation as the quantity that drives the gain adaptation. They prove a general convergence result, propose guidelines to practical implementation and show simulation results for an example. [less ▲]

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See detailA Comparison of Semantic Models for Noninterference
van der Meyden, R.; Zhang, Chenyi UL

in Theoretical Computer Science (2010), 411(47), 41234147

The literature on definitions of security based on causality-like notions such as noninterference has used several distinct semantic models for systems. Early work was based on state machine and trace-set ... [more ▼]

The literature on definitions of security based on causality-like notions such as noninterference has used several distinct semantic models for systems. Early work was based on state machine and trace-set definitions; more recent work has dealt with definitions of security in two distinct process algebraic settings. Comparisons between the definitions has been carried out mainly within semantic frameworks. This paper studies the relationship between semantic frameworks, by defining mappings between a number of semantic models and studying the relationship between notions of noninterference under these mappings. [less ▲]

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See detailNumerical Solution of Non-Isothermal Fluid Flows Using Local Radial Basis Functions (LRBF) Interpolation and a Velocity-Correction Method
Bourantas, Georgios UL; Skouras, Eugene; Loukopoulos, Vasilis et al

in Computer Modeling in Engineering and Sciences (2010), 64(2), 187-212

Meshfree point collocation method (MPCM) is developed, solving the velocity-vorticity formulation of Navier-Stokes equations, for two-dimensional, steady state incompressible viscous flow problems in the ... [more ▼]

Meshfree point collocation method (MPCM) is developed, solving the velocity-vorticity formulation of Navier-Stokes equations, for two-dimensional, steady state incompressible viscous flow problems in the presence of heat transfer. Particular emphasis is placed on the application of the velocity-correction method, ensuring the continuity equation. The Gaussian Radial Basis Functions (GRBF) interpolation is employed to construct the shape functions in conjunction with the framework of the point collocation method. The cases of forced, natural and mixed convection in a 2D rectangular enclosure are examined. The accuracy and the sta- bility of the proposed scheme are demonstrated through three representative, well known and established benchmark problems. Results are presented for high values of the characteristics non-dimensional numbers of the flow, that is, the Reynolds, the Rayleigh and the Richardson number [less ▲]

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See detailA cost-effective atomic force microscope for undergraduate control laboratories
Jones, C. N.; Goncalves, Jorge UL

in IEEE Transactions on Education (2010), 53(2), 328-334

This paper presents a simple, cost-effective and robust atomic force microscope (AFM), which has been purposely designed and built for use as a teaching aid in undergraduate controls labs. The guiding ... [more ▼]

This paper presents a simple, cost-effective and robust atomic force microscope (AFM), which has been purposely designed and built for use as a teaching aid in undergraduate controls labs. The guiding design principle is to have all components be open and visible to the students, so the inner functioning of the microscope has been made clear to see. All of the parts but one are off the shelf, and assembly time is generally less than two days, which makes the microscope a robust instrument that is readily handled by the students with little chance of damage. While the scanning resolution is nowhere near that of a commercial instrument, it is more than sufficient to take interesting scans of micrometer-scale objects. A survey of students after their having used the AFM resulted in a generally good response, with 80% agreeing that they had a positive learning experience. [less ▲]

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See detailMeshfree Point Collocation Schemes for 2D Steady State Incompressible Navier-Stokes Equations in Velocity-Vorticity Formulation for High Values of Reynolds Number
Bourantas, Georgios UL; Skouras, Eugene; Loukopoulos, Vasilios et al

in Computer Modeling in Engineering and Sciences (2010), 59(1), 31-63

A meshfree point collocation method has been developed for the velocity- vorticity formulation of two-dimensional, steady state incompressible Navier-Stokes equations. Particular emphasis was placed on ... [more ▼]

A meshfree point collocation method has been developed for the velocity- vorticity formulation of two-dimensional, steady state incompressible Navier-Stokes equations. Particular emphasis was placed on the application of the velocity-correc- tion method, ensuring the continuity equation. The Moving Least Squares (MLS) approximation is employed for the construction of the shape functions, in conjunc- tion with the general framework of the point collocation method. Computations are obtained for regular and irregular nodal distributions, stressing the positivity con- ditions that make the matrix of the system stable and convergent. The accuracy and the stability of the proposed scheme are demonstrated through two representative, well-known, and established benchmark problems. The numerical scheme was also applied to a case with irregular geometry for marginally high Reynolds numbers [less ▲]

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See detailAn internal version of epistemic logic
Aucher, Guillaume UL

in Studia Logica (2010), 94(1), 1-22

Representing an epistemic situation involving several agents obviously depends on the modeling point of view one takes. We start by identifying the types of modeling points of view which are logically ... [more ▼]

Representing an epistemic situation involving several agents obviously depends on the modeling point of view one takes. We start by identifying the types of modeling points of view which are logically possible. We call the one traditionally followed by epistemic logic the perfect external approach, because there the modeler is assumed to be an omniscient and external observer of the epistemic situation. In the rest of the paper we focus on what we call the internal approach, where the modeler is one of the agents involved in the situation. For this approach we propose and axiomatize a logical formalism based on epistemic logic. This leads us to formalize some intuitions about the internal approach and about its connections with the external ones. Finally, we show that our internal logic is decidable and PSPACE-complete. [less ▲]

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See detailMonostability and multistability of genetic regulatory networks with different types of regulation functions
Pan, Wei UL; Wang, Z; Gao, H. et al

in Nonlinear Analysis: Real World Applications (2010), 11(4), 31703185

Monostability and multistability are proven to be two important topics in synthesis biology and system biology. In this paper, both monostability and multistability are analyzed in a unified framework by ... [more ▼]

Monostability and multistability are proven to be two important topics in synthesis biology and system biology. In this paper, both monostability and multistability are analyzed in a unified framework by applying control theory and mathematical tools. The genetic regulatory networks (GRNs) with multiple time-varying delays and different types of regulation functions are considered. By putting forward a general sector-like regulation function and utilizing up-to-date techniques, a novel Lyapunov–Krasovskii functional is introduced for achieving delay dependence to ensure less conservatism. A new condition is then proposed for the general stability of a GRN in the form of linear matrix inequalities (LMIs) that are dependent on the upper and lower bounds of the delays. Our general stability conditions are applicable to several frequently used regulation functions. It is shown that the existing results for monostability of GRNs are special cases of our main results. Five examples are employed to illustrate the applicability and usefulness of the developed theoretical results. [less ▲]

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See detailAn alternative alpha finite element method (AαFEM) for free and forced structural vibration using triangular meshes
Nguyen-Thanh, N.; Rabczuk, Timon; Nguyen-Xuan, H. et al

in Journal of Computational and Applied Mathematics (2010), 233(9), 2112-2135

An alternative alpha finite element method (AαFEM) using triangular elements is proposed that significantly improves the accuracy of the standard triangular finite elements and provides a superconvergent ... [more ▼]

An alternative alpha finite element method (AαFEM) using triangular elements is proposed that significantly improves the accuracy of the standard triangular finite elements and provides a superconvergent solution in the energy norm for the static analysis of two-dimensional solid mechanics problems. In the AαFEM, the piecewise constant strain field of linear triangular FEM models is enhanced by additional strain terms with an adjustable parameter α which results in an effectively softer stiffness formulation compared to a linear triangular element. The element is further extended to the free and forced vibration analyses of solids. Several numerical examples show that the AαFEM achieves high reliability compared to other existing elements in the literature. [less ▲]

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See detailPANEL: Position-based Aggregator Node Election in Wireless Sensor Networks
Buttyán, Levente; Schaffer, Peter UL

in International Journal of Distributed Sensor Networks (2010), 2010

We introduce PANEL a position-based aggregator node election protocol for wireless sensor networks. The novelty of PANEL with respect to other aggregator node election protocols is that it supports ... [more ▼]

We introduce PANEL a position-based aggregator node election protocol for wireless sensor networks. The novelty of PANEL with respect to other aggregator node election protocols is that it supports asynchronous sensor network applications where the sensor readings are fetched by the base stations after some delay. In particular, the motivation for the design of PANEL was to support reliable and persistent data storage applications, such as TinyPEDS; see the study by Girao et al. (2007). PANEL ensures load balancing, and it supports intra and intercluster routing allowing sensor-to-aggregator, aggregator-to-aggregator, base station-to-aggregator, and aggregator to-base station communications. We also compare PANEL with HEED; see the study by Younis and Fahmy (2004) in the simulation environment provided by TOSSIM, and show that, on one hand, PANEL creates more cohesive clusters than HEED, and, on the other hand, that PANEL is more energy efficient than HEED. [less ▲]

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See detailOn the approximation in the smoothed finite element method (SFEM)
Bordas, Stéphane UL; Natarajan, S.

in International Journal for Numerical Methods in Engineering (2010), 81(5), 660-670

This letter aims at resolving the issues raised in the recent short communication (Int. J. Numer. Meth. Engng 2008; 76(8):1285-1295. DOI: 10.1002/nme.2460) and answered by (Int. J. Numer. Meth. Engng 2009 ... [more ▼]

This letter aims at resolving the issues raised in the recent short communication (Int. J. Numer. Meth. Engng 2008; 76(8):1285-1295. DOI: 10.1002/nme.2460) and answered by (Int. J. Numer. Meth. Engng 2009; DOI: 10.1002/nme.2587) by proposing a systematic approximation scheme based on non-mapped shape functions, which both allows to fully exploit the unique advantages of the smoothed finite element method (SFEM) (Comput. Mech. 2007; 39(6):859-877. DOI: 10.1007/s00466-006-0075-4; Commun. Numer. Meth. Engng 2009; 25(1):19-34. DOI: 10.1002/cnm.1098; Int. J. Numer. Meth. Engng 2007; 71(8):902-930; Comput. Meth. Appl. Mech. Engng 2008; 198(2):165-177. DOI: 10.1016/j.cma.2008.05.029; Comput. Meth. Appl. Mech. Engng 2007; submitted; Int. J. Numer. Meth. Engng 2008; 74(2):175-208. DOI: 10.1002/nme.2146; Comput. Meth. Appl. Mech. Engng 2008; 197 (13-16):1184-1203. DOI: 10.1016/j.cma.2007.10.008) and resolve the existence, linearity and positivity deficiencies pointed out in (Int. J. Numer. Meth. Engng 2008; 76(8):1285-1295). We show that Wachspress interpolants (A Rational Basis for Function Approximation. Academic Press, Inc.: New York, 1975) computed in the physical coordinate system are very well suited to the SFEM, especially when elements are heavily distorted (obtuse interior angles). The proposed approximation leads to results that are almost identical to those of the SFEM initially proposed in (Comput. Mech. 2007; 39(6):859-877. DOI: 10.1007/s00466-006-0075-4). These results suggest that the proposed approximation scheme forms a strong and rigorous basis for the construction of SFEMs. © 2009 John Wiley & Sons, Ltd. [less ▲]

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See detailIntegrating strong and weak discontinuities without integration subcells and example applications in an XFEM/GFEM framework
Natarajan, S.; Roy Mahapatra, D.; Bordas, Stéphane UL

in International Journal for Numerical Methods in Engineering (2010), 83(3), 269-294

Partition of unity methods, such as the extended finite element method, allows discontinuities to be simulated independently of the mesh (Int. J. Numer. Meth. Engng. 1999; 45:601-620). This eliminates the ... [more ▼]

Partition of unity methods, such as the extended finite element method, allows discontinuities to be simulated independently of the mesh (Int. J. Numer. Meth. Engng. 1999; 45:601-620). This eliminates the need for the mesh to be aligned with the discontinuity or cumbersome re-meshing, as the discontinuity evolves. However, to compute the stiffness matrix of the elements intersected by the discontinuity, a subdivision of the elements into quadrature subcells aligned with the discontinuity is commonly adopted. In this paper, we use a simple integration technique, proposed for polygonal domains (Int. J. Numer. Meth. Engng 2009; 80(1):103-134. DOI: 10.1002/nme.2589) to suppress the need for element subdivision. Numerical results presented for a few benchmark problems in the context of linear elastic fracture mechanics and a multi-material problem show that the proposed method yields accurate results. Owing to its simplicity, the proposed integration technique can be easily integrated in any existing code. © 2010 John Wiley & Sons, Ltd. [less ▲]

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See detailA node-based smoothed finite element method with stabilized discrete shear gap technique for analysis of Reissner-Mindlin plates
Nguyen-Xuan, H.; Rabczuk, T.; Nguyen-Thanh, N. et al

in Computational Mechanics (2010), 46(5), 679-701

In this paper, a node-based smoothed finite element method (NS-FEM) using 3-node triangular elements is formulated for static, free vibration and buckling analyses of Reissner-Mindlin plates. The discrete ... [more ▼]

In this paper, a node-based smoothed finite element method (NS-FEM) using 3-node triangular elements is formulated for static, free vibration and buckling analyses of Reissner-Mindlin plates. The discrete weak form of the NS-FEM is obtained based on the strain smoothing technique over smoothing domains associated with the nodes of the elements. The discrete shear gap (DSG) method together with a stabilization technique is incorporated into the NS-FEM to eliminate transverse shear locking and to maintain stability of the present formulation.Aso-called node-based smoothed stabilized discrete shear gap method (NS-DSG) is then proposed. Several numerical examples are used to illustrate the accuracy and effectiveness of the present method. [less ▲]

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See detailNumerically determined enrichment functions for the extended finite element method and applications to bi-material anisotropic fracture and polycrystals
Menk, Alexander; Bordas, Stéphane UL

in International Journal for Numerical Methods in Engineering (2010), 83(7), 805-828

Strain singularities appear in many linear elasticity problems. A very fine mesh has to be used in the vicinity of the singularity in order to obtain acceptable numerical solutions with the finite element ... [more ▼]

Strain singularities appear in many linear elasticity problems. A very fine mesh has to be used in the vicinity of the singularity in order to obtain acceptable numerical solutions with the finite element method (FEM). Special enrichment functions describing this singular behavior can be used in the extended finite element method (X-FEM) to circumvent this problem. These functions have to be known in advance, but their analytical form is unknown in many cases. Li et al. described a method to calculate singular strain fields at the tip of a notch numerically. A slight modification of this approach makes it possible to calculate singular fields also in the interior of the structural domain. We will show in numerical experiments that convergence rates can be significantly enhanced by using these approximations in the X-FEM. The convergence rates have been compared with the ones obtained by the FEM. This was done for a series of problems including a polycrystalline structure. [less ▲]

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See detailNormative Multiagent Systems: Guest Editors' Introduction
Boella, Guido; Pigozzi, Gabriella UL; Singh, Munindar P. et al

in Logic Journal of the IGPL (2010), 18(1), 13

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See detailA simple and robust three-dimensional cracking-particle method without enrichment
Rabczuk, T.; Zi, G.; Bordas, Stéphane UL et al

in Computer Methods in Applied Mechanics and Engineering (2010), 199(37-40), 2437-2455

A new robust and efficient approach for modeling discrete cracks in meshfree methods is described. The method is motivated by the cracking-particle method (Rabczuk T., Belytschko T., International Journal ... [more ▼]

A new robust and efficient approach for modeling discrete cracks in meshfree methods is described. The method is motivated by the cracking-particle method (Rabczuk T., Belytschko T., International Journal for Numerical Methods in Engineering, 2004) where the crack is modeled by a set of cracked segments. However, in contrast to the above mentioned paper, we do not introduce additional unknowns in the variational formulation to capture the displacement discontinuity. Instead, the crack is modeled by splitting particles located on opposite sides of the associated crack segments and we make use of the visibility method in order to describe the crack kinematics. We apply this method to several two- and three-dimensional problems in statics and dynamics and show through several numerical examples that the method does not show any "mesh" orientation bias. © 2010 Elsevier B.V. [less ▲]

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See detailOn multistability of delayed genetic regulatory networks with multivariable regulation functions
Pan, Wei UL; Wang, Z.; Gao, H. et al

in Mathematical Biosciences (2010), 228(1), 100-109

Many genetic regulatory networks (GRNs) have the capacity to reach different stable states. This capacity is defined as multistability which is an important regulation mechanism. Multiple time delays and ... [more ▼]

Many genetic regulatory networks (GRNs) have the capacity to reach different stable states. This capacity is defined as multistability which is an important regulation mechanism. Multiple time delays and multivariable regulation functions are usually inevitable in such GRNs. In this paper, multistability of GRNs is analyzed by applying the control theory and mathematical tools. This study is to provide a theoretical tool to facilitate the design of synthetic gene circuit with multistability in the perspective of control theory. By transforming such GRNs into a new and uniform mathematical formulation, we put forward a general sector-like regulation function that is capable of quantifying the regulation effects in a more precise way. By resorting to up-to-date techniques, a novel Lyapunov–Krasovskii functional (LKF) is introduced for achieving delay dependence to ensure less conservatism. New conditions are then proposed to ensure the multistability of a GRN in the form of linear matrix inequalities (LMIs) that are dependent on the delays. Our multistability conditions are applicable to several frequently used regulation functions especially the multivariable ones. Two examples are employed to illustrate the applicability and usefulness of the developed theoretical results. [less ▲]

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See detailCorrect biological timing in Arabidopsis requires multiple light-signaling pathways.
Dalchau, N.; Hubbard, K. E.; Robertson, F. C. et al

in Proceedings of the National Academy of Sciences of the United States of America (2010), 107(29), 13171-13176

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We ... [more ▼]

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control. [less ▲]

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See detailMultistability of genetic regulatory networks
Pan, Wei UL; Zhang, Z.; Liu, H.

in International Journal of Systems Science (2010), 41(1), 107-118

Multistability is found to be an important recurring theme in synthesis biology. In this article, the multistability analysis problem is investigated by applying control theory and mathematical tools ... [more ▼]

Multistability is found to be an important recurring theme in synthesis biology. In this article, the multistability analysis problem is investigated by applying control theory and mathematical tools. Both the modelling and analysis issues are discussed. Specifically, the genetic regulatory networks (GRNs) with multistability are modelled as switched systems with interval time-varying delays and parameter uncertainties, where the piecewise-affine models are used to approximate the inherent non-linearities existing in the GRNs. Then, by using a novel Lyapunov functional approach and linear matrix inequality (LMI) techniques, a few delay-dependent criteria for the multistability of such genetic regulatory networks are established in the form of LMIs, which can be readily verified by using standard numerical software. A three-component network and a genetic toggle switch with bistability are employed to illustrate the applicability and usefulness of the developed theoretical results. [less ▲]

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See detailRobust H∞ feedback control for uncertain stochastic delayed genetic regulatory networks with additive and multiplicative noise
Pan, Wei UL; Wang, Z.; Gao, H. et al

in International Journal of Robust and Nonlinear Control (2010), 20(18), 2093-2107

Noises are ubiquitous in genetic regulatory networks (GRNs). Gene regulation is inherently a stochastic process because of intrinsic and extrinsic noises that cause kinetic parameter variations and basal ... [more ▼]

Noises are ubiquitous in genetic regulatory networks (GRNs). Gene regulation is inherently a stochastic process because of intrinsic and extrinsic noises that cause kinetic parameter variations and basal rate disturbance. Time delays are usually inevitable due to different biochemical reactions in such GRNs. In this paper, a delayed stochastic model with additive and multiplicative noises is utilized to describe stochastic GRNs. A feedback gene controller design scheme is proposed to guarantee that the GRN is mean-square asymptotically stable with noise attenuation, where the structure of the controllers can be specified according to engineering requirements. By applying control theory and mathematical tools, the analytical solution to the control design problem is given, which helps to provide some insight into synthetic biology and systems biology. The control scheme is employed in a three-gene network to illustrate the applicability and usefulness of the design. [less ▲]

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See detailOn three-dimensional modelling of crack growth using partition of unity methods
Rabczuk, Timon; Bordas, Stéphane UL; Zi, Goangseup

in Computers and Structures (2010), 88(23-24), 1391-1411

This paper reviews different crack tracking techniques in three-dimensions applicable in the context of partition of unity methods, especially meshfree methods. Issues such as describing and tracking the ... [more ▼]

This paper reviews different crack tracking techniques in three-dimensions applicable in the context of partition of unity methods, especially meshfree methods. Issues such as describing and tracking the crack surface are addressed. A crack tracking procedure is proposed in detail and implemented in the context of the extended element-free Galerkin method (XEFG). Several three-dimensional cracking examples are compared to other results from the literature or the experimental data and show good agreement. [less ▲]

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See detailAnalysis of thermoelastic waves in a two-dimensional functionally graded materials domain by the Meshless Local Petrov-Galerkin (MLPG) method
Ahmad Akbari, R.; Bagri, Akbar; Bordas, Stéphane UL et al

in Computer Modeling in Engineering and Sciences (2010), 65(1), 27-74

This contribution focuses on the simulation of two-dimensional elastic wave propagation in functionally graded solids and structures. Gradient volume fractions of the constituent materials are assumed to ... [more ▼]

This contribution focuses on the simulation of two-dimensional elastic wave propagation in functionally graded solids and structures. Gradient volume fractions of the constituent materials are assumed to obey the power law function of position in only one direction and the effective mechanical properties of the material are determined by the Mori–Tanaka scheme. The investigations are carried out by extending a meshless method known as the Meshless Local Petrov-Galerkin (MLPG) method which is a truly meshless approach to thermo-elastic wave propagation. Simulations are carried out for rectangular domains under transient thermal loading. To investigate the effect of material composition on the dynamic response of functionally graded materials, a metal/ceramic (Aluminum (Al) and Alumina (Al2O3) are considered as ceramic and metal constituents) composite is considered for which the transient thermal field, dynamic displacement and stress fields are reported for different material distributions. [less ▲]

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See detailStrain smoothing in FEM and XFEM
Bordas, Stéphane UL; Rabczuk, T.; Hung, N.-X. et al

in Computers and Structures (2010), 88(23-24), 1419-1443

We present in this paper recent achievements realised on the application of strain smoothing in finite elements and propose suitable extensions to problems with discontinuities and singularities. The ... [more ▼]

We present in this paper recent achievements realised on the application of strain smoothing in finite elements and propose suitable extensions to problems with discontinuities and singularities. The numerical results indicate that for 2D and 3D continuum, locking can be avoided. New plate and shell formulations that avoid both shear and membrane locking are also briefly reviewed. The principle is then extended to partition of unity enrichment to simplify numerical integration of discontinuous approximations in the extended finite element method. Examples are presented to test the new elements for problems involving cracks in linear elastic continua and cracked plates. In the latter case, the proposed formulation suppresses locking and yields elements which behave very well, even in the thin plate limit. Two important features of the set of elements presented are their insensitivity to mesh distortion and a lower computational cost than standard finite elements for the same accuracy. These elements are easily implemented in existing codes since they only require the modification of the discretized gradient operator, B. © 2008 Elsevier Ltd. All rights reserved. [less ▲]

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See detailA cell-based smoothed finite element method for kinematic limit analysis
Le, Canh. V.; Nguyen-Xuan, H.; Askes, H. et al

in International Journal for Numerical Methods in Engineering (2010), 83(12), 1651-1674

This paper presents a new numerical procedure for kinematic limit analysis problems, which incorporates the cell-based smoothed finite element method with second-order cone programming. The application of ... [more ▼]

This paper presents a new numerical procedure for kinematic limit analysis problems, which incorporates the cell-based smoothed finite element method with second-order cone programming. The application of a strain smoothing technique to the standard displacement finite element both rules out volumetric locking and also results in an efficient method that can provide accurate solutions with minimal computational effort. The non-smooth optimization problem is formulated as a problem of minimizing a sum of Euclidean norms, ensuring that the resulting optimization problem can be solved by an efficient second-order cone programming algorithm. Plane stress and plane strain problems governed by the von Mises criterion are considered, but extensions to problems with other yield criteria having a similar conic quadratic form or 3D problems can be envisaged. [less ▲]

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See detailA Linear Programming Approach to Parameter Fitting for the Master Equation
Martins, N. C.; Goncalves, Jorge UL

in IEEE Transactions on Automatic Control (2009), 54(10), 2451-2455

This technical note proposes a new framework for the design of continuous time, finite state space Markov processes. In particular, we propose a paradigm for selecting an optimal matrix within a pre ... [more ▼]

This technical note proposes a new framework for the design of continuous time, finite state space Markov processes. In particular, we propose a paradigm for selecting an optimal matrix within a pre-specified pencil of transition rate matrices. Given any transition rate matrix specifying the time-evolution of the Markov process, we propose a class of figures of merit that upper-bounds the long-term evolution of any statistical moment. We show that optimization with respect to the aforementioned class of cost functions is tractable via dualization and linear programming methods. In addition, we suggest how this approach can be used as a tool for the sub-optimal design of the master equation, with performance guarantees. Our results are applied to illustrative examples. [less ▲]

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See detailAdaptive support domain implementation on the Moving Least Squares approximation for Mfree methods applied on elliptic and parabolic PDE problems using strong-form description
Bourantas, Georgios UL; Skouras, Eugene; Nikiforidis, George

in Computer Modeling in Engineering and Sciences (2009), 43

The extent of application of meshfree methods based on point collocation (PC) techniques with adaptive support domain for strong form Partial Differential Equations (PDE) is investigated. The basis ... [more ▼]

The extent of application of meshfree methods based on point collocation (PC) techniques with adaptive support domain for strong form Partial Differential Equations (PDE) is investigated. The basis functions are constructed using the Moving Least Square (MLS) approximation. The weak-form description of PDEs is used in most MLS methods to circumvent problems related to the increased level of resolution necessary near natural (Neumann) boundary conditions (BCs), dislocations, or regions of steep gradients. Alternatively, one can adopt Radial Basis Function (RBF) approximation on the strong-form of PDEs using meshless PC methods, due to the delta function behavior (exact solution on nodes). The present approach is one of the few successful attempts of using MLS approximation [Atluri, Liu, and Han (2006), Han, Liu, Rajendran and Atluri (2006), Atluri and Liu (2006)] instead of RBF approximation for the meshless PC method using strong-form description. To increase the accuracy of the MLS interpolation method and its robustness in problems with natural BCs, a suitable support domain should be chosen in order to ensure an optimized area of coverage for interpolation. To this end, the basis functions are constructed using two different approaches, pertinent to the dimension of the support domain. On one hand, a compact form for the support domain is retained by keeping its radius constant. On the other hand, one can control the number of neighboring nodes as the support domain of each point. The results show that some inaccuracies are present near the boundaries using the first approach, due to the limited number of nodes belonging to the support domain, which results in failed matrix inversion. Instead, the second approach offers capability for fully matrix inversion under many (if not all) circumstances, resulting in basis functions of increased accuracy and robustness. This PC method, applied along with an intelligent adaptive refinement, is demonstrated for elliptic and for parabolic PDEs, related to many flow and mass transfer problems. [less ▲]

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See detailAn accurate, stable and efficient domain-type meshless method for the solution of MHD flow problems
Bourantas, Georgios UL; Skouras, Eugene; Loukopoulos, Vasilios et al

in Journal of Computational Physics (2009), 228

The aim of the present paper is the development of an efficient numerical algorithm for the solution of magnetohydrodynamics flow problems for regular and irregular geometries subject to Dirichlet ... [more ▼]

The aim of the present paper is the development of an efficient numerical algorithm for the solution of magnetohydrodynamics flow problems for regular and irregular geometries subject to Dirichlet, Neumann and Robin boundary conditions. Toward this, the meshless point collocation method (MPCM) is used for MHD flow problems in channels with fully insulating or partially insulating and partially conducting walls, having rectangular, circu- lar, elliptical or even arbitrary cross sections. MPC is a truly meshless and computationally efficient method. The maximum principle for the discrete harmonic operator in the mesh- free point collocation method has been proven very recently, and the convergence proof for the numerical solution of the Poisson problem with Dirichlet boundary conditions have been attained also. Additionally, in the present work convergence is attained for Neumann and Robin boundary conditions, accordingly. The shape functions are constructed using the Moving Least Squares (MLS) approximation. The refinement procedure with meshless methods is obtained with an easily handled and fully automated manner. We present results for Hartmann number up to 105 . The numerical evidences of the proposed meshless method demonstrate the accuracy of the solutions after comparing with the exact solution and the conventional FEM and BEM, for the Dirichlet, Neumann and Robin boundary con- ditions of interior problems with simple or complex boundaries. [less ▲]

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See detailA localized mixed-hybrid method for imposing interfacial constraints in the extended finite element method (XFEM)
Zilian, Andreas UL; Fries, T.-P.

in International Journal for Numerical Methods in Engineering (2009), 79(6), 733-752

The paper proposes an approach for the imposition of constraints along moving or fixed immersed interfaces in the context of the extended finite element method. An enriched approximation space enables ... [more ▼]

The paper proposes an approach for the imposition of constraints along moving or fixed immersed interfaces in the context of the extended finite element method. An enriched approximation space enables consistent representation of strong and weak discontinuities in the solution fields along arbitrarily-shaped material interfaces using an unfitted background mesh. The use of Lagrange multipliers or penalty methods is circumvented by a localized mixed hybrid formulation of the model equations. In a defined region in the vicinity of the interface, the original problem is re-stated in its auxiliary formulation. The availability of the auxiliary variable enables the consideration of a variety of interface constraints in the weak form. The contribution discusses the weak imposition of Dirichlet- and Neumann-type interface conditions as well as continuity requirements not fulfilled a priori by the enriched approximation. The properties of the proposed approach applied to two-dimensional linear scalar- and vector-valued elliptic problems are investigated by studying the convergence behavior. © 2009 John Wiley & Sons,Ltd. [less ▲]

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See detailProjection-based reduction of fluid-structure interaction systems using monolithic space-time modes
Zilian, Andreas UL; Dinkler, D.; Vehre, A.

in Computer Methods in Applied Mechanics and Engineering (2009), 198(47-48), 3795-3805

The focus of this work is the development of reduced models for engineering applications in complex bidirectional fluid-structure interaction. In the simultaneous solution procedure, velocity variables ... [more ▼]

The focus of this work is the development of reduced models for engineering applications in complex bidirectional fluid-structure interaction. In the simultaneous solution procedure, velocity variables are used for both fluid and solid, and the whole set of model equations is discretized by a stabilized time-discontinuous space-time finite element method. Flexible structures are modeled using a three-dimensional continuum approach in a total Lagrangian setting considering large displacements and rotations. In the flow domain the incompressible Navier-Stokes equations describe the Newtonian fluid. A continuous finite element mesh is applied to the entire spatial domain, and the discretized model equations are assembled in a single set of algebraic equations, considering the two-field problem as a whole. The continuous fluid-structure mesh with identical orders of approximation for both solid and fluid in space and time automatically yields conservation of mass, momentum and energy at the fluid-structure interface. A mesh-moving scheme is used to adapt the nodal coordinates of the fluid space-time finite element mesh to the structural deformation. The computational approach for strongly coupled fluid-structure interaction is used to create suitable reduced models of generic nonlinear problems. Reduction is performed with monolithic projection-based space-time modes, ensuring strong coupling of fluid and structure in the reduced model. The contribution discusses results using proper orthogonal decomposition (POD) for determination of monolithic space-time modes in the reduction of fluid-structure systems. © 2009 Elsevier B.V. All rights reserved. [less ▲]

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See detailTemperature Fields Induced by Low Power Focused Ultrasound in Soft Tissues During Gene Therapy. Numerical Predictions and Experimental Results
Gambin, Barbara; Kujawska, Tamara; Kruglenko, Eleonora et al

in Archives of Acoustics (2009), 34(4), 445459

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See detailAddressing volumetric locking and instabilities by selective integration in smoothed finite elements
Hung, Nguyen-Xuan; Bordas, Stéphane UL; Hung, Nguyen-Dang

in Communications in Numerical Methods in Engineering (2009), 25(1), 19-34

This paper promotes the development of a novel family of finite elements with smoothed strains, offering remarkable properties. In the smoothed finite element method (FEM), elements are divided into ... [more ▼]

This paper promotes the development of a novel family of finite elements with smoothed strains, offering remarkable properties. In the smoothed finite element method (FEM), elements are divided into subcells. The strain at a point is defined as a weighted average of the standard strain field over a representative domain. This yields superconvergent stresses, both in regular and singular settings, as well as increased accuracy, with slightly lower computational cost than the standard FEM. The one-subcell version that does not exhibit volumetric locking yields more accurate stresses but less accurate displacements and is equivalent to a quasi-equilibrium FEM. It is also subject to instabilities. In the limit where the number of subcells goes to infinity, the standard FEM is recovered, which yields more accurate displacements and less accurate stresses. The specific contribution of this paper is to show that expressing the volumetric part of the strain field using a one-subcell formulation is sufficient to get rid of volumetric locking and increase the displacement accuracy compared with the standard FEM when the single subcell version is used to express both the volumetric and deviatoric parts of the strain. Selective integration also alleviates instabilities associated with the single subcell element, which are due to rank deficiency. Numerical examples on various compressible and incompressible linear elastic test cases show that high accuracy is retained compared with the standard FEM without increasing computational cost. [less ▲]

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See detailOn time integration in the XFEM
Fries, T.-P.; Zilian, Andreas UL

in International Journal for Numerical Methods in Engineering (2009), 79(1), 69-93

The extended finite element method (XFEM) is often used in applications that involve moving interfaces. Examples are the propagation of cracks or the movement of interfaces in two-phase problems. This ... [more ▼]

The extended finite element method (XFEM) is often used in applications that involve moving interfaces. Examples are the propagation of cracks or the movement of interfaces in two-phase problems. This work focuses on time integration in the XFEM. The performance of the discontinuous Galerkin method in time (space-time finite elements (FEs)) and time-stepping schemes are analyzed by convergence studies for different model problems. It is shown that space-time FE achieve optimal convergence rates. Special care is required for time stepping in the XFEM due to the time dependence of the enrichment functions. In each time step, the enrichment functions have to be evaluated at different time levels. This has important consequences in the quadrature used for the integration of the weak form. A time-stepping scheme that leads to optimal or only slightly sub-optimal convergence rates is systematically constructed in this work. © 2009 John Wiley & Sons, Ltd. [less ▲]

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See detailNumerical integration over arbitrary polygonal domains based on Schwarz-Christoffel conformal mapping
Natarajan, S.; Bordas, Stéphane UL; Roy mahapatra, D.

in International Journal for Numerical Methods in Engineering (2009), 80(1), 103-134

This paper presents a new numerical integration technique on arbitrary polygonal domains. The polygonal domain is mapped conformally to the unit disk using Schwarz-Christoffel mapping and a midpoint ... [more ▼]

This paper presents a new numerical integration technique on arbitrary polygonal domains. The polygonal domain is mapped conformally to the unit disk using Schwarz-Christoffel mapping and a midpoint quadrature rule defined on this unit disk is used. This method eliminates the need for a two-level isoparametric mapping usually required. Moreover, the positivity of the Jacobian is guaranteed. Numerical results presented for a few benchmark problems in the context of polygonal finite elements show that the proposed method yields accurate results. © 2009 John Wiley & Sons, Ltd. [less ▲]

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See detailReachability analysis of continuous-time piecewise affine systems
Hamadeh, A. O.; Goncalves, Jorge UL

in Automatica (2008), 44(12), 3189-3194

This paper proposes an algorithm for the characterization of reachable sets of states for continuous-time piecewise affine systems. Given a model of the system and a bounded set of possible initial states ... [more ▼]

This paper proposes an algorithm for the characterization of reachable sets of states for continuous-time piecewise affine systems. Given a model of the system and a bounded set of possible initial states, the algorithm employs an LMI approach to compute both upper and lower bounds on reachable regions. Rather than performing computations in the state-space, this method uses impact maps to find the reachable sets on the switching surfaces of the system. This tool can then be used to deduce safety and performance results about the system. [less ▲]

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See detailNecessary and sufficient conditions for dynamical structure reconstruction of LTI networks
Goncalves, Jorge UL; Warnick, S.

in IEEE Transactions on Automatic Control (2008), 53(7), 1670-1674

This paper formulates and solves the network reconstruction problem for linear time-invariant systems. The problem is motivated from a variety of disciplines, but it has recently received considerable ... [more ▼]

This paper formulates and solves the network reconstruction problem for linear time-invariant systems. The problem is motivated from a variety of disciplines, but it has recently received considerable attention from the systems biology community in the study of chemical reaction networks. Here, we demonstrate that even when a transfer function can be identified perfectly from input–output data, not even Boolean reconstruction is possible, in general, without more information about the system.We then completely characterize this additional information that is essential for dynamical reconstruction without appeal to ad-hoc assumptions about the network, such as sparsity or minimality. [less ▲]

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See detailComputational representation and hemodynamic characterization of in vivo acquired severe stenotic renal artery geometries using turbulence modeling
Kagadis, George; Skouras, Eugene; Bourantas, Georgios UL et al

in Medical Engineering and Physics (2008), 30(5), 647-660

The present study reports on computational fluid dynamics in the case of severe renal artery stenosis (RAS). An anatomically realistic model of a renal artery was reconstructed from CT scans, and used to ... [more ▼]

The present study reports on computational fluid dynamics in the case of severe renal artery stenosis (RAS). An anatomically realistic model of a renal artery was reconstructed from CT scans, and used to conduct CFD simulations of blood flow across RAS. The recently developed Shear Stress Transport turbulence model was pivotally applied in the simulation of blood flow in the region of interest. Blood flow was studied in vivo under the presence of RAS and subsequently in simulated cases before the development of RAS, and after endovascular stent implantation. The pressure gradients in the RAS case were many orders of magnitude larger than in the healthy case. The presence of RAS increased flow resistance, which led to considerably lower blood flow rates. A simulated stent in place of the RAS decreased the flow resistance at levels proportional to, and even lower than, the simulated healthy case without the RAS. The wall shear stresses, differential pressure profiles, and net forces exerted on the surface of the atherosclerotic plaque at peak pulse were shown to be of relevant high distinctiveness, so as to be considered potential indicators of hemodynamically significant RAS. [less ▲]

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See detailBimodal and hysteretic expression in mammalian cells from a synthetic gene circuit
May, T.; Eccleston, L. J.; Markusic, D. et al

in Public Library of Science ONE (2008), 3(6),

In order to establish cells and organisms with predictable properties, synthetic biology makes use of controllable, synthetic genetic devices. These devices are used to replace or to interfere with ... [more ▼]

In order to establish cells and organisms with predictable properties, synthetic biology makes use of controllable, synthetic genetic devices. These devices are used to replace or to interfere with natural pathways. Alternatively, they may be interlinked with endogenous pathways to create artificial networks of higher complexity. While these approaches have been already successful in prokaryotes and lower eukaryotes, the implementation of such synthetic cassettes in mammalian systems and even animals is still a major obstacle. This is mainly due to the lack of methods that reliably and efficiently transduce synthetic modules without compromising their regulation properties. To pave the way for implementation of synthetic regulation modules in mammalian systems we utilized lentiviral transduction of synthetic modules. A synthetic positive feedback loop, based on the Tetracycline regulation system was implemented in a lentiviral vector system and stably integrated in mammalian cells. This gene regulation circuit yields a bimodal expression response. Based on experimental data a mathematical model based on stochasticity was developed which matched and described the experimental findings. Modelling predicted a hysteretic expression responsewhich was verified experimentally. Thereby supporting the idea that the system is driven by stochasticity. The results presented here highlight that the combination of three independent tools/methodologies facilitate the reliable installation of synthetic gene circuits with predictable expression characteristics in mammalian cells and organisms. [less ▲]

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See detailA smoothed finite element method for shell analysis
Nguyen-Thanh, N.; Rabczuk, T.; Nguyen-Xuan, H. et al

in Computer Methods in Applied Mechanics and Engineering (2008), 198(2), 165-177

A four-node quadrilateral shell element with smoothed membrane-bending based on Mindlin-Reissner theory is proposed. The element is a combination of a plate bending and membrane element. It is based on ... [more ▼]

A four-node quadrilateral shell element with smoothed membrane-bending based on Mindlin-Reissner theory is proposed. The element is a combination of a plate bending and membrane element. It is based on mixed interpolation where the bending and membrane stiffness matrices are calculated on the boundaries of the smoothing cells while the shear terms are approximated by independent interpolation functions in natural coordinates. The proposed element is robust, computationally inexpensive and free of locking. Since the integration is done on the element boundaries for the bending and membrane terms, the element is more accurate than the MITC4 element for distorted meshes. This will be demonstrated for several numerical examples. [less ▲]

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See detailMeshless methods: A review and computer implementation aspects
Nguyen, V. P.; Rabczuk, T.; Bordas, Stéphane UL et al

in Mathematics and Computers in Simulation (2008), 79(3), 763-813

The aim of this manuscript is to give a practical overview of meshless methods (for solid mechanics) based on global weak forms through a simple and well-structured MATLAB code, to illustrate our ... [more ▼]

The aim of this manuscript is to give a practical overview of meshless methods (for solid mechanics) based on global weak forms through a simple and well-structured MATLAB code, to illustrate our discourse. The source code is available for download on our website and should help students and researchers get started with some of the basic meshless methods; it includes intrinsic and extrinsic enrichment, point collocation methods, several boundary condition enforcement schemes and corresponding test cases. Several one and two-dimensional examples in elastostatics are given including weak and strong discontinuities and testing different ways of enforcing essential boundary conditions. © 2008 IMACS. [less ▲]

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See detailA smoothed finite element method for plate analysis
Nguyen-Xuan, H.; Rabczuk, T.; Bordas, Stéphane UL et al

in Computer Methods in Applied Mechanics and Engineering (2008), 197(13-16), 1184-1203

A quadrilateral element with smoothed curvatures for Mindlin-Reissner plates is proposed. The curvature at each point is obtained by a non-local approximation via a smoothing function. The bending ... [more ▼]

A quadrilateral element with smoothed curvatures for Mindlin-Reissner plates is proposed. The curvature at each point is obtained by a non-local approximation via a smoothing function. The bending stiffness matrix is calculated by a boundary integral along the boundaries of the smoothing elements (smoothing cells). Numerical results show that the proposed element is robust, computational inexpensive and simultaneously very accurate and free of locking, even for very thin plates. The most promising feature of our elements is their insensitivity to mesh distortion. [less ▲]

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See detailA simple error estimator for extended finite elements
Bordas, Stéphane UL; Duflot, Marc; Le, Phong

in Communications in Numerical Methods in Engineering (2008), 24(11), 961-971

This short communication presents the idea of an a posteriori error estimate for enriched (extended) finite elements (XFEM). The enhanced strain field against which the XFEM strains are compared, is ... [more ▼]

This short communication presents the idea of an a posteriori error estimate for enriched (extended) finite elements (XFEM). The enhanced strain field against which the XFEM strains are compared, is computed through extended moving least-squares smoothing constructed using the diffraction method to preserve the discontinuity. The error estimator is the L2 norm of the difference of the XFEM strain with the enhanced strain. We prove the concept of the proposed method on a 1D example with a singular solution and a 2D fracture mechanics example and conclude with some future work based on our paradigm. [less ▲]

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See detailA combined extended finite element and level set method for biofilm growth
Duddu, Ravindra; Bordas, Stéphane UL; Chopp, David et al

in International Journal for Numerical Methods in Engineering (2008), 74(5), 848-870

This paper presents a computational technique based on the extended finite element method (YFEM) and the level set method for the growth of biofilms. The discontinuous-derivative enrichment of the ... [more ▼]

This paper presents a computational technique based on the extended finite element method (YFEM) and the level set method for the growth of biofilms. The discontinuous-derivative enrichment of the standard finite element approximation eliminates the need for the finite element mesh to coincide with the biofilm-fluid interface and also permits the introduction of the discontinuity in the normal derivative of the substrate concentration field at the biofilm-fluid interface. The XFEM is coupled with a comprehensive level set update scheme with velocity extensions, which makes updating the biofilm interface fast and accurate without need for remeshing. The kinetics of biofilms are briefly given and the non-linear strong and weak forms are presented. The non-linear system of equations is solved using a Newton-Raphson scheme. Example problems including 1D and 2D biofilm growth are presented to illustrate the accuracy and utility of the method. The 1D results we obtain are in excellent agreement with previous 1D results obtained using finite difference methods. Our 2D results that simulate finger formation and finger-tip splitting in biofilms illustrate the robustness of the present computational technique. [less ▲]

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See detailThree-dimensional crack initiation, propagation, branching and junction in non-linear materials by an extended meshfree method without asymptotic enrichment
Bordas, Stéphane UL; Rabczuk, Timon; Zi, Goangseup

in Engineering Fracture Mechanics (2008), 75(5), 943-960

This paper presents a three-dimensional, extrinsically enriched meshfree method for initiation, branching, growth and coalescence of an arbitrary number of cracks in non-linear solids including large ... [more ▼]

This paper presents a three-dimensional, extrinsically enriched meshfree method for initiation, branching, growth and coalescence of an arbitrary number of cracks in non-linear solids including large deformations, for statics and dynamics. The novelty of the methodology is that only an extrinsic discontinuous enrichment and no near-tip enrichment is required. Instead, a Lagrange multiplier field is added along the crack front to close the crack. This decreases the computational cost and removes difficulties involved with a branch enrichment. The results are compared to experimental data, and other simulations from the literature to show the robustness and accuracy of the method. [less ▲]

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See detailA geometrically non-linear three-dimensional cohesive crack method for reinforced concrete structures
Rabczuk, Timon; Zi, Goangseup; Bordas, Stéphane UL et al

in Engineering Fracture Mechanics (2008), 75(16), 4740-4758

A three-dimensional meshfree method for modeling arbitrary crack initiation and crack growth in reinforced concrete structure is presented. This meshfree method is based on a partition of unity concept ... [more ▼]

A three-dimensional meshfree method for modeling arbitrary crack initiation and crack growth in reinforced concrete structure is presented. This meshfree method is based on a partition of unity concept and formulated for geometrically non-linear problems. The crack kinematics are obtained by enriching the solution space in order to capture the correct crack kinematics. A cohesive zone model is used after crack initiation. The reinforcement modeled by truss or beam elements is connected by a bond model to the concrete. We applied the method to model the fracture of several reinforced concrete structures and compared the results to experimental data. [less ▲]

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See detailA posteriori error estimation for extended finite elements by an extended global recovery
Duflot, M.; Bordas, Stéphane UL

in International Journal for Numerical Methods in Engineering (2008), 76(8), 1123-1138

This contribution presents an extended global derivative recovery for enriched finite element methods (FEMs), such as the extended FEM along with an associated error indicator. Owing to its simplicity ... [more ▼]

This contribution presents an extended global derivative recovery for enriched finite element methods (FEMs), such as the extended FEM along with an associated error indicator. Owing to its simplicity, the proposed scheme is ideally suited to industrial applications. The procedure is based on global minimization of the L2 norm of the difference between the raw strain field (C-1) and the recovered (C0) strain field. The methodology engineered in this paper extends the ideas of Oden and Brauchli (Int. J. Numer. Meth. Engng 1971; 3) and Hinton and Campbell (Int. J. Numer. Meth. Engng 1974; 8) by enriching the approximation used for the construction of the recovered derivatives (strains) with the gradients of the functions employed to enrich the approximation employed for the primal unknown (displacements). We show linear elastic fracture mechanics examples, both in simple two-dimensional settings, and for a three-dimensional structure. Numerically, we show that the effectivity index of the proposed indicator converges to unity upon mesh refinement. Consequently, the approximate error converges to the exact error, indicating that the error indicator is valid. Additionally, the numerical examples suggest a novel adaptive strategy for enriched approximations in which the dimensions of the enrichment zone are first increased, before standard h- and p-adaptivities are applied; we suggest to coin this methodology e-adaptivity. Copyright © 2008 John Wiley & Sons, Ltd. [less ▲]

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See detailEnergieaudit Schul -und Sportkomplex Roodt/Syre
Scheuren, Jean-Jacques UL; Scholzen, Frank UL

in Revue Technique Luxembourgeoise (2008), Heft 2-2008

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See detailThe Arabidopsis circadian clock incorporates a cADPR-based feedback loop
Dodd, A. N.; Gardner, M. J.; Hotta, C. T. et al

in SCIENCE (2007), 318(5857), 1789-1792

Transcriptional feedback loops are a feature of circadian clocks in both animals and plants. We show that the plant circadian clock also incorporates the cytosolic signaling molecule cyclic adenosine ... [more ▼]

Transcriptional feedback loops are a feature of circadian clocks in both animals and plants. We show that the plant circadian clock also incorporates the cytosolic signaling molecule cyclic adenosine diphosphate ribose (cADPR). cADPR modulates the circadian oscillator’s transcriptional feedback loops and drives circadian oscillations of Ca2+ release. The effects of antagonists of cADPR signaling, manipulation of cADPR synthesis, and mathematical simulation of the interaction of cADPR with the circadian clock indicate that cADPR forms a feedback loop within the plant circadian clock. [less ▲]

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See detailA three-dimensional meshfree method for continuous multiple-crack initiation, propagation and junction in statics and dynamics
Rabczuk, Timon; Bordas, Stéphane UL; Zi, Goangseup

in Computational Mechanics (2007), 40(3), 473-495

This paper proposes a three-dimensional meshfree method for arbitrary crack initiation and propagation that ensures crack path continuity for non-linear material models and cohesive laws. The method is ... [more ▼]

This paper proposes a three-dimensional meshfree method for arbitrary crack initiation and propagation that ensures crack path continuity for non-linear material models and cohesive laws. The method is based on a local partition of unity. An extrinsic enrichment of the meshfree shape functions is used with discontinuous and near-front branch functions to close the crack front and improve accuracy. The crack is hereby modeled as a jump in the displacement field. The initiation and propagation of a crack is determined by the loss of hyperbolicity or the loss of material stability criterion. The method is applied to several static, quasi-static and dynamic crack problems. The numerical results very precisely replicate available experimental and analytical results. [less ▲]

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See detailDerivative recovery and a posteriori error estimate for extended finite elements
Bordas, Stéphane UL; Duflot, M.

in Computer Methods in Applied Mechanics and Engineering (2007), 196(35-36), 3381-3399

This paper is the first attempt at error estimation for extended finite elements. The goal of this work is to devise a simple and effective local a posteriori error estimate for partition of unity ... [more ▼]

This paper is the first attempt at error estimation for extended finite elements. The goal of this work is to devise a simple and effective local a posteriori error estimate for partition of unity enriched finite element methods such as the extended finite element method (XFEM). In each element, the local estimator is the L2 norm of the difference between the raw XFEM strain field and an enhanced strain field computed by extended moving least squares (XMLS) derivative recovery obtained from the raw nodal XFEM displacements. The XMLS construction is tailored to the nature of the solution. The technique is applied to linear elastic fracture mechanics, in which near-tip asymptotic functions are added to the MLS basis. The XMLS shape functions are constructed from weight functions following the diffraction criterion to represent the discontinuity. The result is a very smooth enhanced strain solution including the singularity at the crack tip. Results are shown for two- and three-dimensional linear elastic fracture mechanics problems in mode I and mixed mode. The effectivity index of the estimator is close to 1 and improves upon mesh refinement for the studied near-tip problem. It is also shown that for the linear elastic fracture mechanics problems treated, the proposed estimator outperforms one of the superconvergent patch recovery technique of Zienkiewicz and Zhu, which is only C0. Parametric studies of the general performance of the estimator are also carried out. © 2007 Elsevier B.V. All rights reserved. [less ▲]

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See detailA simulation-based design paradigm for complex cast components
Bordas, Stéphane UL; Conley, James. G.; Moran, Brian et al

in Engineering with Computers (2007), 23(1), 25-37

This paper describes and exercises a new design paradigm for cast components. The methodology integrates foundry process simulation, non-destructive evaluation (NDE), stress analysis and damage tolerance ... [more ▼]

This paper describes and exercises a new design paradigm for cast components. The methodology integrates foundry process simulation, non-destructive evaluation (NDE), stress analysis and damage tolerance simulations into the design process. Foundry process simulation is used to predict an array of porosity-related anomalies. The probability of detection of these anomalies is investigated with a radiographic inspection simulation tool (XRSIM). The likelihood that the predicted array of anomalies will lead to a failure is determined by a fatigue crack growth simulation based on the extended finite element method and therefore does not require meshing nor remeshing as the cracks grow. With this approach, the casting modeling provides initial anomaly information, the stress analysis provides a value for the critical size of an anomaly and the NDE assessment provides a detectability measure. The combination of these tools allows for accept/reject criteria to be determined at the early design stage and enables damage tolerant design philosophies. The methodology is applied to the design of a cast monolithic door used on the Boeing 757 aircraft. [less ▲]

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