BlackNUFFT: Modular customizable black box hybrid parallelization of type 3 NUFFT in 3D

Many applications benefit from an efficient Discrete Fourier Transform (DFT) between arbitrarily spaced points. The Non Uniform Fast Fourier Transform reduces the computational cost of such operation from to exploiting gridding algorithms and a standard Fast Fourier Transform on an equi-spaced grid. The parallelization of the NUFFT of type 3 (between arbitrary points in space and frequency) still poses some challenges: we present a novel and flexible hybrid parallelization in a MPI-multithreaded environment exploiting existing HPC libraries on modern architectures. To ensure the reliability of the developed library, we exploit continuous integration strategies using Travis CI. We present performance analyses to prove the effectiveness of our implementation, possible extensions to the existing library, and an application of NUFFT type 3 to MRI image processing

Modelling Fluid Structure Interaction problems using Boundary Element Method

This dissertation investigates the application of Boundary Element Methods (BEM) to Fluid Structure Interaction (FSI) problems under three main different perspectives. This work is divided in three main parts: i) the derivation of BEM for the Laplace equation and its application to analyze ship-wave interaction problems, ii) the imple- mentation of efficient and parallel BEM solvers addressing the newest challenges of High Performance Computing, iii) the developing of a BEM for the Stokes system and its application to study micro-swimmers.First we develop a BEM for the Laplace equation and we apply it to predict ship-wave interactions making use of an innovative coupling with Finite Element Method stabilization techniques. As well known, the wave pattern around a body depends on the Froude number associated to the flow. Thus, we throughly investigate the robustness and accuracy of the developed methodology assessing the solution dependence on such parameter. To improve the performance and tackle problems with higher number of unknowns, the BEM developed for the Laplace equation is parallelized using OpenSOURCE tech- nique in a hybrid distributed-shared memory environment. We perform several tests to demonstrate both the accuracy and the performance of the parallel BEM developed. In addition, we explore two different possibilities to reduce the overall computational cost from O(N2) to O(N). Firstly we couple the library with a Fast Multiple Method that allows us to reach for higher order of complexity and efficiency. Then we perform a preliminary study on the implementation of a parallel Non Uniform Fast Fourier Transform to be coupled with the newly developed algorithm Sparse Cardinal Sine De- composition (SCSD).Finally we consider the application of the BEM framework to a different kind of FSI problem represented by the Stokes flow of a liquid medium surrounding swimming micro-organisms. We maintain the parallel structure derived for the Laplace equation even in the Stokes setting. Our implementation is able to simulate both prokaryotic and eukaryotic organisms, matching literature and experimental benchmarks. We finally present a deep analysis of the importance of hydrodynamic interactions between the different parts of micro-swimmers in the prevision of optimal swimming conditions, focusing our attention on the study of flagellated \u201crobotic\u201d composite swimmers

New acquisitions in the physiopathology of multiple myeloma: role of the bone microenvironment

Multiple myeloma (MM) is a plasma cell malignancy characterized by the accumulation of malignant plasma cells within the bone marrow (BM). MM cells interact with the microenvironment and induce pathological modifications that in turn support the growth and survival of MM cells. The BM microenvironment consists of various extracellular matrix proteins, and cell components as haematopoietic stem cells, progenitor and precursor cells, immune cells, erythrocytes, BM stromal cells (BMSCs), BM endothelial cells, as well as osteoclasts and osteoblasts that are able to secret several growth factors for MM cells. The direct interactions of MM cells with the microenvironment and the secreted cytokines activate signalling pathways mediating growth, survival, drug resistance and the migration of MM cells as well as osteoclastogenesis and angiogenesis. In this article we underline in particular the new evidences at the basis of the interaction between MM cell and bone cells and the potential role of osteoclast and osteoblast in MM pathophysiology. O mieloma múltiplo (MM) é uma doença maligna das células plasmáticas caracterizada pelo acúmulo de células plasmáticas na medula óssea (MO). As células do MM interagem com o microambiente e induzem modificações patológicas que, por seu turno, propiciam o crescimento e a sobrevida das células do MM. O microambiente da MO consiste de várias proteínas da matriz extracelular e de componentes hematopoéticos: células-tronco, progenitoras e precursoras, células imunes, eritrocitárias, estromais, endoteliais. Possuem também osteoclastos e osteoblastos capazes de secreção de fatores de crescimento das células do MM. A direta interação das células mielomatosas com o microambiente e a secreção de citocinas ativam cascatas sinalizadoras que mediam o crescimento, sobrevida, resistência a drogas e a migração destas células assim como a osteoclastogênese e a angiogênese. Neste artigo explicitamos novas evidências e as bases da interação das células mielomatosas e as células medulares e o provável papel dos osteoclastos e dos osteoblastos na fisiopatologia do MM

Angiogenic switch in multiple myeloma.

Angiogenesis is the hallmark of cancer. Growing evidence indicates that an imbalance between pro- and anti-angiogenic molecules triggers the angiogenic switch during tumor progression. Several molecules, able to affect vascular formation and function, are now beginning to be elucidated. Recent data indicate that angiogenesis also occurs in hematological malignancies. In multiple myeloma it has been demonstrated that patients with active disease have an increase in bone marrow angiogenesis correlated with the progression of disease and an adverse prognosis. The pathophysiology of myeloma-induced angiogenesis is complex and involves either the direct production of angiogenic molecules by myeloma cells or their induction in the microenvironment. In this review we have focalized our attention on the main factors involved in the angiogenic switch that occurs in MM patients

The Challenge of Measuring Corporate Social Irresponsibility

In this paper, we develop a family of indexes to measure the social irresponsibility of firms. We define corporate social irresponsibility (CSIR) on the basis of firms’ alleged involvement in human rights abuses. After a critical appraisal of the existing CSIR raw data and measures/indexes, we take a M-quantile regression approach to develop a family of CSIR indexes that overcome the limitations of existing measures. We apply our methodology to a sample of 380 large publicly-listed firms, observed over the period 2004-2012. Our analysis develops a family of CSIR indexes robust to firms’ media exposure, size and industry specificities, and provides a measure of their accurac

Biology and Treatment of Multiple Myeloma

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Predicting and Optimizing Microswimmer Performance from the Hydrodynamics of Its Components: The Relevance of Interactions

Interest in the design of bioinspired robotic microswimmers is growing rapidly, motivated by the spectacular capabilities of their unicellular biological templates. Predicting the swimming speed and efficiency of such devices in a reliable way is essential for their rational design, and to optimize their performance. The hydrodynamic simulations needed for this purpose are demanding and simplified models that neglect nonlocal hydrodynamic interactions (e.g., resistive force theory for slender, filament-like objects that are the typical propulsive apparatus for unicellular swimmers) are commonly used. We show through a detailed case study of a model robotic system consisting of a spherical head powered by a rotating helical flagellum that (a) the errors one makes in the prediction of swimming speed and efficiency by neglecting hydrodynamic interactions are never quite acceptable and (b) there are simple ways to correct the predictions of the simplified theories to make them more accurate. We also formulate optimal design problems for the length of the helical flagellum giving maximal energetic efficiency, maximal distance traveled per motor turn, or maximal distance traveled per unit of work expended, and exhibit optimal solutions

A unified steady and unsteady formulation for hydrodynamic potential flow simulations with fully nonlinear free surface boundary conditions

This work discusses the correct modeling of the fully nonlinear free surface boundary conditions to be prescribed in water waves flow simulations based on potential flow theory. The main goal of such a discussion is that of identifying a mathematical formulation and a numerical treatment that can be used both to carry out transient simulations, and to compute steady solutions -- for any flow admitting them. In the literature on numerical towing tank in fact, steady and unsteady fully nonlinear potential flow solvers are characterized by different mathematical formulations. The kinematic and dynamic fully nonlinear free surface boundary conditions are discussed, and in particular it is proven that the kinematic free surface boundary condition, written in semi-Lagrangian form, can be manipulated to derive an alternative non penetration boundary condition by all means identical to the one used on the surface of floating bodies or on the basin bottom. The simplified mathematical problem obtained is discretized over space and time via Boundary Element Method (BEM) and Implicit Backward Difference Formula (BDF) scheme, respectively. The results confirm that the solver implemented is able to solve steady potential flow problems just by eliminating null time derivatives in the unsteady formulation. Numerical results obtained confirm that the solver implemented is able to accurately reproduce results of classical steady flow solvers available in the literature.Comment: The final version of the present paper has been accepted for publication on Applied Mathematical Modellin

Deal2lkit: a Toolkit Library for High Performance Programming in deal.II

We propose a software design for the efficient and flexible handling of the building blocks used in high performance finite element simulations, through the pervasive use of parameters (parsed through parameter files). In the proposed design, all the building blocks of a high performance finite element program are built according to the command and composite design patterns.We present version 1.1.0 of the deal2lkit (deal.II ToolKit) library, which is a collection of modules and classes aimed at providing high level interfaces to several deal.II classes and functions, obeying the command and composite design patterns, and controlled via parameter files. Keywords: Object-orientation, Software design, Finite element methods, C+