112 research outputs found

    Riemannian geometry for efficient analysis of protein dynamics data

    Full text link
    An increasingly common viewpoint is that protein dynamics data sets reside in a non-linear subspace of low conformational energy. Ideal data analysis tools for such data sets should therefore account for such non-linear geometry. The Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich structure to account for a wide range of geometries that can be modelled after an energy landscape. Second, many standard data analysis tools initially developed for data in Euclidean space can also be generalised to data on a Riemannian manifold. In the context of protein dynamics, a conceptual challenge comes from the lack of a suitable smooth manifold and the lack of guidelines for constructing a smooth Riemannian structure based on an energy landscape. In addition, computational feasibility in computing geodesics and related mappings poses a major challenge. This work considers these challenges. The first part of the paper develops a novel local approximation technique for computing geodesics and related mappings on Riemannian manifolds in a computationally feasible manner. The second part constructs a smooth manifold of point clouds modulo rigid body group actions and a Riemannian structure that is based on an energy landscape for protein conformations. The resulting Riemannian geometry is tested on several data analysis tasks relevant for protein dynamics data. It performs exceptionally well on coarse-grained molecular dynamics simulated data. In particular, the geodesics with given start- and end-points approximately recover corresponding molecular dynamics trajectories for proteins that undergo relatively ordered transitions with medium sized deformations. The Riemannian protein geometry also gives physically realistic summary statistics and retrieves the underlying dimension even for large-sized deformations within seconds on a laptop

    IgA-BEM for 3D Helmholtz problems using conforming and non-conforming multi-patch discretizations and B-spline tailored numerical integration

    Get PDF
    An Isogeometric Boundary Element Method (IgA-BEM) is considered for the numerical solution of Helmholtz problems on 3D bounded or unbounded domains, admitting a smooth multi-patch representation of their finite boundary surface. The discretization spaces are formed by C0 inter-patch continuous functional spaces whose restriction to a patch simplifies to the span of tensor product B-splines composed with the given patch NURBS parameterization. Both conforming and non-conforming spaces are allowed, so that local refinement is possible at the patch level. For regular and singular integration, the proposed model utilizes a numerical procedure defined on the support of each trial B-spline function, which makes possible a function-by-function implementation of the matrix assembly phase. Spline quasi-interpolation is the common ingredient of all the considered quadrature rules; in the singular case it is combined with a B-spline recursion over the spline degree and with a singularity extraction technique, extended to the multi-patch setting for the first time. A threshold selection strategy is proposed to automatically distinguish between nearly singular and regular integrals. The non-conforming C0 joints between spline spaces on different patches are implemented as linear constraints based on knot removal conditions, and do not require a hierarchical master-slave relation between neighbouring patches. Numerical examples on relevant benchmarks show that the expected convergence orders are achieved with uniform discretization and a small number of uniformly spaced quadrature nodes

    The Construction of Optimized High-Order Surface Meshes by Energy-Minimization

    Get PDF
    Despite the increasing popularity of high-order methods in computational fluid dynamics, their application to practical problems still remains challenging. In order to exploit the advantages of high-order methods with geometrically complex computational domains, coarse curved meshes are necessary, i.e. high-order representations of the geometry. This dissertation presents a strategy for the generation of curved high-order surface meshes. The mesh generation method combines least-squares fitting with energy functionals, which approximate physical bending and stretching energies, in an incremental energy-minimizing fitting strategy. Since the energy weighting is reduced in each increment, the resulting surface representation features high accuracy. Nevertheless, the beneficial influence of the energy-minimization is retained. The presented method aims at enabling the utilization of the superior convergence properties of high-order methods by facilitating the construction of coarser meshes, while ensuring accuracy by allowing an arbitrary choice of geometric approximation order. Results show surface meshes of remarkable quality, even for very coarse meshes representing complex domains, e.g. blood vessels

    System- and Data-Driven Methods and Algorithms

    Get PDF
    An increasing complexity of models used to predict real-world systems leads to the need for algorithms to replace complex models with far simpler ones, while preserving the accuracy of the predictions. This two-volume handbook covers methods as well as applications. This first volume focuses on real-time control theory, data assimilation, real-time visualization, high-dimensional state spaces and interaction of different reduction techniques

    Mathematical Modeling and Simulation in Mechanics and Dynamic Systems

    Get PDF
    The present book contains the 16 papers accepted and published in the Special Issue “Mathematical Modeling and Simulation in Mechanics and Dynamic Systems” of the MDPI “Mathematics” journal, which cover a wide range of topics connected to the theory and applications of Modeling and Simulation of Dynamic Systems in different field. These topics include, among others, methods to model and simulate mechanical system in real engineering. It is hopped that the book will find interest and be useful for those working in the area of Modeling and Simulation of the Dynamic Systems, as well as for those with the proper mathematical background and willing to become familiar with recent advances in Dynamic Systems, which has nowadays entered almost all sectors of human life and activity

    Mathematical Modelling of Energy Systems and Fluid Machinery

    Get PDF
    The ongoing digitalization of the energy sector, which will make a large amount of data available, should not be viewed as a passive ICT application for energy technology or a threat to thermodynamics and fluid dynamics, in the light of the competition triggered by data mining and machine learning techniques. These new technologies must be posed on solid bases for the representation of energy systems and fluid machinery. Therefore, mathematical modelling is still relevant and its importance cannot be underestimated. The aim of this Special Issue was to collect contributions about mathematical modelling of energy systems and fluid machinery in order to build and consolidate the base of this knowledge

    Combining Parameterizations, Sobolev Methods and Shape Hessian Approximations for Aerodynamic Design Optimization

    Get PDF
    Aerodynamic design optimization, considered in this thesis, is a large and complex area spanning different disciplines from mathematics to engineering. To perform optimizations on industrially relevant test cases, various algorithms and techniques have been proposed throughout the literature, including the Sobolev smoothing of gradients. This thesis combines the Sobolev methodology for PDE constrained flow problems with the parameterization of the computational grid and interprets the resulting matrix as an approximation of the reduced shape Hessian. Traditionally, Sobolev gradient methods help prevent a loss of regularity and reduce high-frequency noise in the derivative calculation. Such a reinterpretation of the gradient in a different Hilbert space can be seen as a shape Hessian approximation. In the past, such approaches have been formulated in a non-parametric setting, while industrially relevant applications usually have a parameterized setting. In this thesis, the presence of a design parameterization for the shape description is explicitly considered. This research aims to demonstrate how a combination of Sobolev methods and parameterization can be done successfully, using a novel mathematical result based on the generalized FaĂ  di Bruno formula. Such a formulation can yield benefits even if a smooth parameterization is already used. The results obtained allow for the formulation of an efficient and flexible optimization strategy, which can incorporate the Sobolev smoothing procedure for test cases where a parameterization describes the shape, e.g., a CAD model, and where additional constraints on the geometry and the flow are to be considered. Furthermore, the algorithm is also extended to One Shot optimization methods. One Shot algorithms are a tool for simultaneous analysis and design when dealing with inexact flow and adjoint solutions in a PDE constrained optimization. The proposed parameterized Sobolev smoothing approach is especially beneficial in such a setting to ensure a fast and robust convergence towards an optimal design. Key features of the implementation of the algorithms developed herein are pointed out, including the construction of the Laplace-Beltrami operator via finite elements and an efficient evaluation of the parameterization Jacobian using algorithmic differentiation. The newly derived algorithms are applied to relevant test cases featuring drag minimization problems, particularly for three-dimensional flows with turbulent RANS equations. These problems include additional constraints on the flow, e.g., constant lift, and the geometry, e.g., minimal thickness. The Sobolev smoothing combined with the parameterization is applied in classical and One Shot optimization settings and is compared to other traditional optimization algorithms. The numerical results show a performance improvement in runtime for the new combined algorithm over a classical Quasi-Newton scheme

    Advanced Techniques for Design and Manufacturing in Marine Engineering

    Get PDF
    Modern engineering design processes are driven by the extensive use of numerical simulations; naval architecture and ocean engineering are no exception. Computational power has been improved over the last few decades; therefore, the integration of different tools such as CAD, FEM, CFD, and CAM has enabled complex modeling and manufacturing problems to be solved in a more feasible way. Classical naval design methodology can take advantage of this integration, giving rise to more robust designs in terms of shape, structural and hydrodynamic performances, and the manufacturing process.This Special Issue invites researchers and engineers from both academia and the industry to publish the latest progress in design and manufacturing techniques in marine engineering and to debate the current issues and future perspectives in this research area. Suitable topics for this issue include, but are not limited to, the following:CAD-based approaches for designing the hull and appendages of sailing and engine-powered boats and comparisons with traditional techniques;Finite element method applications to predict the structural performance of the whole boat or of a portion of it, with particular attention to the modeling of the material used;Embedded measurement systems for structural health monitoring;Determination of hydrodynamic efficiency using experimental, numerical, or semi-empiric methods for displacement and planning hulls;Topology optimization techniques to overcome traditional scantling criteria based on international standards;Applications of additive manufacturing to derive innovative shapes for internal reinforcements or sandwich hull structures

    3D Reconstruction Using High Resolution Implicit Surface Representations and Memory Management Strategies

    Get PDF
    La disponibilité de capteurs de numérisation 3D rapides et précis a permis de capturer de très grands ensembles de points à la surface de différents objets qui véhiculent la géométrie des objets. La métrologie appliquée consiste en l'application de mesures dans différents domaines tels que le contrôle qualité, l'inspection, la conception de produits et la rétroingénierie. Une fois que le nuage de points 3D non organisés couvrant toute la surface de l'objet a été capturé, un modèle de la surface doit être construit si des mesures métrologiques doivent être effectuées sur l'objet. Dans la reconstruction 3D en temps réel, à l'aide de scanners 3D portables, une représentation de surface implicite très efficace est le cadre de champ vectoriel, qui suppose que la surface est approchée par un plan dans chaque voxel. Le champ vectoriel contient la normale à la surface et la matrice de covariance des points tombant à l'intérieur d'un voxel. L'approche globale proposée dans ce projet est basée sur le cadre Vector Field. Le principal problème abordé dans ce projet est la résolution de l'incrément de consommation de mémoire et la précision du modèle reconstruit dans le champ vectoriel. Ce tte approche effectue une sélection objective de la taille optimale des voxels dans le cadre de champ vectoriel pour maintenir la consommation de mémoire aussi faible que possible et toujours obtenir un modèle précis de la surface. De plus, un ajustement d e surface d'ordre élevé est utilisé pour augmenter la précision du modèle. Étant donné que notre approche ne nécessite aucune paramétrisation ni calcul complexe, et qu'au lieu de travailler avec chaque point, nous travaillons avec des voxels dans le champ vectoriel, cela réduit la complexité du calcul.The availability of fast and accurate 3D scanning sensors has made it possible to capture very large sets of points at the surface of different objects that convey the geometry of the objects. A pplied metrology consists in the application of measurements in different fields such as quality control, inspection, product design and reverse engineering. Once the cloud of unorganized 3D points covering the entire surface of the object has been capture d, a model of the surface must be built if metrologic measurements are to be performed on the object. In realtime 3D reconstruction, using handheld 3D scanners a very efficient implicit surface representation is the Vector Field framework, which assumes that the surface is approximated by a plane in each voxel. The vector field contains the normal to the surface and the covariance matrix of the points falling inside a voxel. The proposed global approach in this project is based on the Vector Field framew ork. The main problem addressed in this project is solving the memory consumption increment and the accuracy of the reconstructed model in the vector field. This approach performs an objective selection of the optimal voxels size in the vector field frame work to keep the memory consumption as low as possible and still achieve an accurate model of the surface. Moreover, a highorder surface fitting is used to increase the accuracy of the model. Since our approach do not require any parametrization and compl ex calculation, and instead of working with each point we are working with voxels in the vector field, then it reduces the computational complexity

    Mesh-Free and Finite Element-Based Methods for Structural Mechanics Applications

    Get PDF
    The problem of solving complex engineering problems has always been a major topic in all industrial fields, such as aerospace, civil and mechanical engineering. The use of numerical methods has increased exponentially in the last few years, due to modern computers in the field of structural mechanics. Moreover, a wide range of numerical methods have been presented in the literature for solving such problems. Structural mechanics problems are dealt with using partial differential systems of equations that might be solved by following the two main classes of methods: Domain-decomposition methods or the so-called finite element methods and mesh-free methods where no decomposition is carried out. Both methodologies discretize a partial differential system into a set of algebraic equations that can be easily solved by computer implementation. The aim of the present Special Issue is to present a collection of recent works on these themes and a comparison of the novel advancements of both worlds in structural mechanics applications
    • …
    corecore