The LifeV library: engineering mathematics beyond the proof of concept

LifeV is a library for the finite element (FE) solution of partial differential equations in one, two, and three dimensions. It is written in C++ and designed to run on diverse parallel architectures, including cloud and high performance computing facilities. In spite of its academic research nature, meaning a library for the development and testing of new methods, one distinguishing feature of LifeV is its use on real world problems and it is intended to provide a tool for many engineering applications. It has been actually used in computational hemodynamics, including cardiac mechanics and fluid-structure interaction problems, in porous media, ice sheets dynamics for both forward and inverse problems. In this paper we give a short overview of the features of LifeV and its coding paradigms on simple problems. The main focus is on the parallel environment which is mainly driven by domain decomposition methods and based on external libraries such as MPI, the Trilinos project, HDF5 and ParMetis. Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar

Comparison of shape parametrization techniques for fluid-structure interaction problems

This master thesis describes the development in the framework of Fluid- Structure Interaction (FSI) problems of an efficient and flexible technique treating the fluid-structure interface and mesh motion problems. The main idea is to build, through a new hierarchical approach, a tool with accurate identication capabilities for both the structural rigid movement (translation/rotation) and the elastic deformation (displacement), with the possibility of facing arbitrary structural and fluid discretization schemes. Starting from a review of the state of the art methods, used for these applications, the different shape representation techniques applied, like Free Form Deformation (FFD), Radial Basis Function (RBF) and Inverse Distance Weighting (IDW) are introduced and then compared to test their performances in terms of computational costs and achievable mesh quality. Then, in order to reduce the complexity of the geometrical model and its description, ad hoc innovative optimization techniques, like a selective approach of the RBF interpolation sites as well as a domain-decomposition approach for FFD, are presented showing clear reductions in term of computational costs. Some applications and test-cases, solved by using an open-source Finite Element library (LifeV), dealing with unsteady viscous (internal and external) flows, characterized by different Reynolds number, are shown to highlight the quality and the accuracy of the methods and their stability. For the implementation of the schemes developed, an efficient C++ object oriented code language was used, relying also on Trilinos packages

Parallel Algorithms for the Solution of Large-Scale Fluid-Structure Interaction Problems in Hemodynamics

This thesis addresses the development and implementation of efficient and parallel algorithms for the numerical simulation of Fluid-Structure Interaction (FSI) problems in hemodynamics. Indeed, hemodynamic conditions in large arteries are significantly affected by the interaction of the pulsatile blood flow with the arterial wall. The simulation of fluid-structure interaction problems requires the approximation of a coupled system of Partial Differential Equations (PDEs) and the set up of efficient numerical solution strategies. Blood is modeled as an incompressible Newtonian fluid whose dynamics is governed by the Navier-Stokes equations. Different constituive models are used to describe the mechanical response of the arterial wall; specifically, we rely on hyperelastic isotropic and anistotropic material laws. The finite element method is used for the space discretization of both the fluid and structure problems. In particular, for the Navier-Stokes equations we consider a semi-discrete formulation based on the Variational Multiscale (VMS) method. Among a wide range of possible solution strategies for the FSI problem, here we focus on strongly coupled monolithic approaches wherein the nonlinearities are treated in a fully implicit mode. To cope with the high computational complexity of the three dimensional FSI problem, a parallel solution framework is often mandatory. To this end, we develop a new block parallel preconditioner for the coupled linearized FSI system obtained after space and time discretization. The proposed preconditioner, named FaCSI, exploits the factorized form of the FSI Jacobian matrix, the use of static condensation to formally eliminate the interface degrees of freedom of the fluid equations, and the use of a SIMPLE preconditioner for unsteady Navier-Stokes equations. In FSI problems, the different resolution requirements in the fluid and structure physical domains, as well as the presence of complex interface geometries make the use of matching fluid and structure meshes problematic. In such situations, it is much simpler to deal with discretizations that are nonconforming at the interface, provided however that the matching conditions at the interface are properly fulfilled. In this thesis we develop a novel interpolation-based method, named INTERNODES, for numerically solving partial differential equations by Galerkin methods on computational domains that are split into two (or several) subdomains featuring nonconforming interfaces. By this we mean that either a priori independent grids and/or local polynomial degrees are used to discretize each subdomain. INTERNODES can be regarded as an alternative to the mortar element method: it combines the accuracy of the latter with the easiness of implementation in a numerical code. The aforementioned techniques have been applied for the numerical simulation of large-scale fluid-structure interaction problems in the context of biomechanics. The parallel algorithms developed showed scalability up to thousands of cores utilized on high performance computing machines

Study of Holtermanniella wattica, Leucosporidium creatinivorum, Naganishia adeliensis, Solicoccozyma aeria, and Solicoccozyma terricola for their lipogenic aptitude from different carbon sources

Background The ability of some microorganisms to accumulate lipids is well known; however, only recently the number of studies on microbial lipid biosynthesis for obtaining oleochemical products, namely biofuels and some building blocks for chemistry, is rapidly and spectacularly increased. Since 1990s, some oleaginous yeasts were studied for their ability to accumulate lipids up to 60\u201370% of their dry weight. Due to the vast array of engineering techniques currently available, the recombinant DNA technology was the main approach followed so far for obtaining lipid-overproducing yeasts, mainly belonging to the Yarrowia lipolytica. However, an alternative approach can be offered by worldwide diversity as source of novel oleaginous yeasts. Lipogenic aptitude of a number of yeast strains has been reviewed, but many of these studies utilized a limited number of species and/or different culture conditions that make impossible the comparison of different results. Accordingly, the lipogenic aptitude inside the yeast world is still far from being fully explored, and finding new oleaginous yeast species can acquire a strategic importance. Results Holtermanniella wattica, Leucosporidium creatinivorum, Naganishia adeliensis, Solicoccozyma aeria, and Solicoccozyma terricola strains were selected as a result of a large-scale screening on 706 yeasts (both Ascomycota and Basidiomycota). Lipid yields and fatty acid profiles of selected strains were evaluated at 20 and 25 \ub0C on glucose, and on glycerol, xylose, galactose, sucrose, maltose, and cellobiose. A variable fatty acid profile was observed in dependence of both temperature and different carbon sources. On the whole, L. creatinivorum exhibited the highest performances: total lipid yield (YL) >7 g/l on glucose and glycerol, % of intracellular lipids on cell biomass (YL/DW) >70% at 20 \ub0C on glucose, lipid coefficient (YL/Glu) around 20% on glucose, and daily productivity (YL/d) on glucose and sucrose >1.6 g/(l*d). Conclusions This study provides some meaningful information about the lipogenic ability of some yeast species. Variable lipid yields and fatty acid profiles were observed in dependence of both temperature and different carbon sources. L. creatinivorum exhibited the highest lipogenic performances

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at \sqrt{s}=7\TeV

A measurement of the production cross-section for top quark pairs(\ttbar) in $pp$ collisions at \sqrt{s}=7 \TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron $e$ or muon $\mu$) with large missing transverse energy and at least four jets, and dilepton ($ee$, $\mu\mu$ or $e\mu$) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb-1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-\ttbar Standard Model processes are estimated using data-driven methods and determined to be $12.2 \pm 3.9$ events and $2.5 \pm 0.6$ events, respectively. The kinematic properties of the selected events are consistent with SM \ttbar production. The inclusive top quark pair production cross-section is measured to be \sigmattbar=145 \pm 31 ^{+42}_{-27} pb where the first uncertainty is statistical and the second systematic. The measurement agrees with perturbative QCD calculations.Comment: 30 pages plus author list (50 pages total), 9 figures, 11 tables, CERN-PH number and final journal adde

Measurement of the top quark pair cross section with ATLAS in pp collisions at √s=7 TeV using final states with an electron or a muon and a hadronically decaying τ lepton

A measurement of the cross section of top quark pair production in proton-proton collisions recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 7 TeV is reported. The data sample used corresponds to an integrated luminosity of 2.05 fb -1. Events with an isolated electron or muon and a τ lepton decaying hadronically are used. In addition, a large missing transverse momentum and two or more energetic jets are required. At least one of the jets must be identified as originating from a b quark. The measured cross section, σtt-=186±13(stat.)±20(syst.)±7(lumi.) pb, is in good agreement with the Standard Model prediction

Evidence of the association of BIN1 and PICALM with the AD risk in contrasting European populations

Recent genome-wide association studies have identified five loci (BIN1, CLU, CR1, EXOC3L2 and PICALM) as genetic determinants of Alzheimer’s disease (AD). We attempted to confirm the association between these genes and the AD risk in three contrasting European populations (from Finland, Italy and Spain). Since CLU and CR1 had already been analyzed in these populations, we restricted our investigation to BIN1, EXO2CL3 and PICALM. In a total of 2,816 AD cases and 2,706 controls, we unambiguously replicated the association of rs744373 (for BIN1) and rs541458 (for PICALM) polymorphisms with the AD risk (OR=1.26, 95% CI [1.15-1.38], p=2.9x10-7, and OR=0.80, 95% CI [0.74-0.88], p=4.6x10-7, respectively). In a meta-analysis, rs597668 (EXOC3L2) was also associated with the AD risk, albeit to a lesser extent (OR=1.19, 95% CI [1.06-1.32], p=2.0x10-3). However, this signal did not appear to be independent of APOE. In conclusion, we confirmed that BIN1 and PICALM are genetic determinants of AD, whereas the potential involvement of EXOC3L2 requires further investigation