14 research outputs found
Polygonization of Multi-Component Non-Manifold Implicit Surfaces through A Symbolic-Numerical Continuation Algorithm
In computer graphics, most algorithms for sampling implicit surfaces
use a 2-points numerical method. If the surface-describing
function evaluates positive at the first point and negative at the second
one, we can say that the surface is located somewhere between
them. Surfaces detected this way are called sign-variant implicit
surfaces. However, 2-points numerical methods may fail to detect
and sample the surface because the functions of many implicit surfaces
evaluate either positive or negative everywhere around them.
These surfaces are here called sign-invariant implicit surfaces. In
this paper, instead of using a 2-points numerical method, we use a
1-point numerical method to guarantee that our algorithm detects
and samples both sign-variant and sign-invariant surface components
or branches correctly. This algorithm follows a continuation
approach to tessellate implicit surfaces, so that it applies symbolic
factorization to decompose the function expression into symbolic
components, sampling then each symbolic function component separately.
This ensures that our algorithm detects, samples, and triangulates
most components of implicit surfaces
Geometric modeling, simulation, and visualization methods for plasmid DNA molecules
Plasmid DNA molecules are a special type of DNA molecules that are used, among other applications,
in DNA vaccination and gene therapy. These molecules are characterized by, when in
their natural state, presenting a closed-circular conformation and by being supercoiled. The
production of plasmid DNA using bacteria as hosts implies a purification step where the plasmid
DNA molecules are separated from the DNA of the host and other contaminants. This purification
process, and all the physical and chemical variations involved, such as temperature
changes, may affect the plasmid DNA molecules conformation by uncoiling or even by open
them, which makes them useless for therapeutic applications. Because of that, researchers
are always searching for new purification techniques that maximize the amount of supercoiled
plasmid DNA that is produced. Computer simulations and 3D visualization of plasmid DNA can
bring many advantages because they allow researchers to actually see what can happen to the
molecules under certain conditions. In this sense, it was necessary to develop reliable and accurate
geometric models specific for plasmid DNA simulations. This dissertation presents a new
assembling algorithm for B-DNA specifically developed for plasmid DNA assembling. This new
assembling algorithm is completely adaptive in the sense that it allows researchers to assemble
any plasmid DNA base-pair sequence along any arbitrary conformation that fits the length
of the plasmid DNA molecule. This is specially suitable for plasmid DNA simulations, where
conformations are generated by simulation procedures and there is the need to assemble the
given base-pair sequence over that conformation, what can not be done by conventional predictive
DNA assembling methods. Unlike traditional molecular visualization methods that are
based on the atomic structure, this new assembling algorithm uses color coded 3D molecular
surfaces of the nucleotides as the building blocks for DNA assembling. This new approach, not
only reduces the amount of graphical objects and, consequently, makes the rendering faster,
but also makes it easier to visually identify the nucleotides in the DNA strands. The algorithm
used to triangulate the molecular surfaces of the nucleotides building blocks is also a novelty
presented as part of this dissertation. This new triangulation algorithm for Gaussian molecular
surfaces introduces a new mechanism that divides the atomic structure of molecules into boxes
and spheres. This new space division method is faster because it confines the local calculation
of the molecular surface to a specific region of influence of the atomic structure, not taking into
account atoms that do not influence the triangulation of the molecular surface in that region.
This new method also guarantees the continuity of the molecular surface. Having in mind that
the aim of this dissertation is to present a complete set of methods for plasmid DNA visualization
and simulation, it is also proposed a new deformation algorithm to be used for plasmid
DNA Monte Carlo simulations. This new deformation algorithm uses a 3D polyline to represent
the plasmid DNA conformation and performs small deformations on that polyline, keeping the
segments length and connectivity. Experiments have been performed in order to compare this
new deformation method with deformation methods traditionally used by Monte Carlo plasmid
DNA simulations These experiments shown that the new method is more efficient in the sense
that its trial acceptance ratio is higher and it converges sooner and faster to the elastic energy
equilibrium state of the plasmid DNA molecule. In sum, this dissertation successfully presents
an end-to-end set of models and algorithms for plasmid DNA geometric modelling, visualization
and simulation
Renderização de curvas implícitas discretizadas no domínio da imagem
A representação gráfica de curvas implícitas continua a ser um tópico de investigação importante em computação gráfica e geometria computacional, e tem aplicações em várias áreas de interesse como sejam, por exemplo, representação de símbolos em tipografia digital, delimitação de contornos em imagem médica gerada por tomografia axial, bem como na definição de trajetórias para a simulação de movimento de personagens em animação computacional e jogos de vídeo. De forma sumária, pode dizer-se que esta dissertação propõe um algoritmo de pixelização de curvas implícitas que, ao que parece, não tem paralelo na literatura, a não ser nos algoritmos de rasterização de linhas retas e circunferências que incorporavam os sistemas gráficos primitivos, como por exemplo o algoritmo de Bresenham. De alguma maneira, o referido algoritmo de pixelização pode ser visto como uma generalização daqueles algoritmos primitivos no sentido de que se aplica a qualquer curva implícita, mesmo que ela apresente singularidades, pontos isolados, e outros pontos críticos.The graphical representation of implicit curves remains a major research topic in computer
graphics and computational geometry, and has applications in several areas of interest such
as, for example, representation of symbols in digital typography, delineation of contours in
medical images generated by computerized axial tomography, as well as the definition of
trajectories for the simulation of movement of characters in computer animation and video
games.
Briefly speaking, it can be said that this dissertation proposes a pixelization algorithm for
implicit curves that apparently has no parallel in literature, except in the rasterization
algorithms of straight lines and circles incorporated in primitive graphics systems, such as
Bresenham's algorithm. Somehow, this algorithm pixelization can be seen as a generalization
of those primitive algorithms in that it applies to any curve implied, even if it presents
singularities, isolated points, and other critical points
Geometric algorithms for cavity detection on protein surfaces
Macromolecular structures such as proteins heavily empower cellular processes or functions.
These biological functions result from interactions between proteins and peptides,
catalytic substrates, nucleotides or even human-made chemicals. Thus, several
interactions can be distinguished: protein-ligand, protein-protein, protein-DNA,
and so on. Furthermore, those interactions only happen under chemical- and shapecomplementarity
conditions, and usually take place in regions known as binding sites.
Typically, a protein consists of four structural levels. The primary structure of a protein
is made up of its amino acid sequences (or chains). Its secondary structure essentially
comprises -helices and -sheets, which are sub-sequences (or sub-domains) of amino
acids of the primary structure. Its tertiary structure results from the composition of
sub-domains into domains, which represent the geometric shape of the protein. Finally,
the quaternary structure of a protein results from the aggregate of two or more
tertiary structures, usually known as a protein complex.
This thesis fits in the scope of structure-based drug design and protein docking. Specifically,
one addresses the fundamental problem of detecting and identifying protein
cavities, which are often seen as tentative binding sites for ligands in protein-ligand
interactions. In general, cavity prediction algorithms split into three main categories:
energy-based, geometry-based, and evolution-based. Evolutionary methods build upon
evolutionary sequence conservation estimates; that is, these methods allow us to detect
functional sites through the computation of the evolutionary conservation of the
positions of amino acids in proteins. Energy-based methods build upon the computation
of interaction energies between protein and ligand atoms. In turn, geometry-based algorithms
build upon the analysis of the geometric shape of the protein (i.e., its tertiary
structure) to identify cavities. This thesis focuses on geometric methods.
We introduce here three new geometric-based algorithms for protein cavity detection.
The main contribution of this thesis lies in the use of computer graphics techniques
in the analysis and recognition of cavities in proteins, much in the spirit of molecular
graphics and modeling. As seen further ahead, these techniques include field-of-view
(FoV), voxel ray casting, back-face culling, shape diameter functions, Morse theory,
and critical points. The leading idea is to come up with protein shape segmentation,
much like we commonly do in mesh segmentation in computer graphics. In practice,
protein cavity algorithms are nothing more than segmentation algorithms designed for
proteins.Estruturas macromoleculares tais como as proteínas potencializam processos ou funções
celulares. Estas funções resultam das interações entre proteínas e peptídeos, substratos
catalíticos, nucleótideos, ou até mesmo substâncias químicas produzidas pelo
homem. Assim, há vários tipos de interacções: proteína-ligante, proteína-proteína,
proteína-DNA e assim por diante. Além disso, estas interações geralmente ocorrem em
regiões conhecidas como locais de ligação (binding sites, do inglês) e só acontecem sob
condições de complementaridade química e de forma. É também importante referir que
uma proteína pode ser estruturada em quatro níveis. A estrutura primária que consiste
em sequências de aminoácidos (ou cadeias), a estrutura secundária que compreende
essencialmente por hélices e folhas , que são subsequências (ou subdomínios) dos
aminoácidos da estrutura primária, a estrutura terciária que resulta da composição de
subdomínios em domínios, que por sua vez representa a forma geométrica da proteína,
e por fim a estrutura quaternária que é o resultado da agregação de duas ou mais estruturas
terciárias. Este último nível estrutural é frequentemente conhecido por um
complexo proteico.
Esta tese enquadra-se no âmbito da conceção de fármacos baseados em estrutura e no
acoplamento de proteínas. Mais especificamente, aborda-se o problema fundamental
da deteção e identificação de cavidades que são frequentemente vistos como possíveis
locais de ligação (putative binding sites, do inglês) para os seus ligantes (ligands, do
inglês). De forma geral, os algoritmos de identificação de cavidades dividem-se em três
categorias principais: baseados em energia, geometria ou evolução. Os métodos evolutivos
baseiam-se em estimativas de conservação das sequências evolucionárias. Isto é,
estes métodos permitem detectar locais funcionais através do cálculo da conservação
evolutiva das posições dos aminoácidos das proteínas. Em relação aos métodos baseados
em energia estes baseiam-se no cálculo das energias de interação entre átomos
da proteína e do ligante. Por fim, os algoritmos geométricos baseiam-se na análise da
forma geométrica da proteína para identificar cavidades. Esta tese foca-se nos métodos
geométricos.
Apresentamos nesta tese três novos algoritmos geométricos para detecção de cavidades
em proteínas. A principal contribuição desta tese está no uso de técnicas de computação
gráfica na análise e reconhecimento de cavidades em proteínas, muito no espírito da
modelação e visualização molecular. Como pode ser visto mais à frente, estas técnicas
incluem o field-of-view (FoV), voxel ray casting, back-face culling, funções de diâmetro
de forma, a teoria de Morse, e os pontos críticos. A ideia principal é segmentar a
proteína, à semelhança do que acontece na segmentação de malhas em computação
gráfica. Na prática, os algoritmos de detecção de cavidades não são nada mais que
algoritmos de segmentação de proteínas
Proceedings of the ECCOMAS Thematic Conference on Multibody Dynamics 2015
This volume contains the full papers accepted for presentation at the ECCOMAS Thematic Conference on Multibody Dynamics 2015 held in the Barcelona School of Industrial Engineering, Universitat Politècnica de Catalunya, on June 29 - July 2, 2015. The ECCOMAS Thematic Conference on Multibody Dynamics is an international meeting held once every two years in a European country. Continuing the very successful series of past conferences that have been organized in Lisbon (2003), Madrid (2005), Milan (2007), Warsaw (2009), Brussels (2011) and Zagreb (2013); this edition will once again serve as a meeting point for the international researchers, scientists and experts from academia, research laboratories and industry working in the area of multibody dynamics. Applications are related to many fields of contemporary engineering, such as vehicle and railway systems, aeronautical and space vehicles, robotic manipulators, mechatronic and autonomous systems, smart structures, biomechanical systems and nanotechnologies. The topics of the conference include, but are not restricted to: ● Formulations and Numerical Methods ● Efficient Methods and Real-Time Applications ● Flexible Multibody Dynamics ● Contact Dynamics and Constraints ● Multiphysics and Coupled Problems ● Control and Optimization ● Software Development and Computer Technology ● Aerospace and Maritime Applications ● Biomechanics ● Railroad Vehicle Dynamics ● Road Vehicle Dynamics ● Robotics ● Benchmark ProblemsPostprint (published version
Multibody dynamics 2015
This volume contains the full papers accepted for presentation at the ECCOMAS Thematic Conference on Multibody Dynamics 2015 held in the Barcelona School of Industrial Engineering, Universitat Politècnica de Catalunya, on June 29 - July 2, 2015. The ECCOMAS Thematic Conference on Multibody Dynamics is an international meeting held once every two years in a European country. Continuing the very successful series of past conferences that have been organized in Lisbon (2003), Madrid (2005), Milan (2007), Warsaw (2009), Brussels (2011) and Zagreb (2013); this edition will once again serve as a meeting point for the international researchers, scientists and experts from academia, research laboratories and industry working in the area of multibody dynamics. Applications are related to many fields of contemporary engineering, such as vehicle and railway systems, aeronautical and space vehicles, robotic manipulators, mechatronic and autonomous systems, smart structures, biomechanical systems and nanotechnologies. The topics of the conference include, but are not restricted to: Formulations and Numerical Methods, Efficient Methods and Real-Time Applications, Flexible Multibody Dynamics, Contact Dynamics and Constraints, Multiphysics and Coupled Problems, Control and Optimization, Software Development and Computer Technology, Aerospace and Maritime Applications, Biomechanics, Railroad Vehicle Dynamics, Road Vehicle Dynamics, Robotics, Benchmark Problems. The conference is organized by the Department of Mechanical Engineering of the Universitat Politècnica de Catalunya (UPC) in Barcelona. The organizers would like to thank the authors for submitting their contributions, the keynote lecturers for accepting the invitation and for the quality of their talks, the awards and scientific committees for their support to the organization of the conference, and finally the topic organizers for reviewing all extended abstracts and selecting the awards nominees.Postprint (published version
Vibration, Control and Stability of Dynamical Systems
From Preface: This is the fourteenth time when the conference “Dynamical Systems: Theory and Applications” gathers a numerous group of outstanding scientists and engineers, who deal with widely understood problems of theoretical and applied dynamics. Organization of the conference would not have been possible without a great effort of the staff of the Department of Automation, Biomechanics and Mechatronics. The patronage over the conference has been taken by the Committee of Mechanics of the Polish Academy of Sciences and Ministry of Science and Higher Education of Poland. It is a great pleasure that our invitation has been accepted by recording in the history of our conference number of people, including good colleagues and friends as well as a large group of researchers and scientists, who decided to participate in the conference for the first time. With proud and satisfaction we welcomed over 180 persons from 31 countries all over the world. They decided to share the results of their research and many years experiences in a discipline of dynamical systems by submitting many very interesting papers. This year, the DSTA Conference Proceedings were split into three volumes entitled “Dynamical Systems” with respective subtitles: Vibration, Control and Stability of Dynamical Systems; Mathematical and Numerical Aspects of Dynamical System Analysis and Engineering Dynamics and Life Sciences. Additionally, there will be also published two volumes of Springer Proceedings in Mathematics and Statistics entitled “Dynamical Systems in Theoretical Perspective” and “Dynamical Systems in Applications”
Friction Force Microscopy of Deep Drawing Made Surfaces
Aim of this paper is to contribute to micro-tribology understanding and friction in micro-scale
interpretation in case of metal beverage production, particularly the deep drawing process of cans. In order to bridging the gap between engineering and trial-and-error principles, an experimental AFM-based micro-tribological approach is adopted. For that purpose, the can’s surfaces are imaged with atomic force microscopy (AFM) and the frictional force signal is measured with frictional force microscopy (FFM). In both techniques, the sample surface is scanned with a stylus attached to a cantilever. Vertical motion of the cantilever is recorded in AFM and horizontal motion is recorded in FFM. The presented work evaluates friction over a micro-scale on various samples gathered from cylindrical, bottom and round parts of cans, made of same the material but with different deep drawing process parameters. The main idea is to link the experimental observation with the manufacturing process. Results presented here can advance the knowledge in order to comprehend the tribological phenomena at the contact scales, too small for conventional tribology
Towards a Conceptual Design of an Intelligent Material Transport Based on Machine Learning and Axiomatic Design Theory
Reliable and efficient material transport is one of the basic requirements that affect productivity in sheet metal industry. This paper presents a methodology for conceptual design of intelligent material transport using mobile robot, based on axiomatic design theory, graph theory and
artificial intelligence. Developed control algorithm was implemented and tested on the mobile robot system Khepera II within the laboratory model of manufacturing environment. Matlab© software package was used for manufacturing process simulation, implementation of search algorithms and neural network training. Experimental results clearly show that intelligent mobile robot can learn and predict optimal material transport flows thanks to the use of artificial neural networks. Achieved positioning error of mobile robot indicates that conceptual design approach can be used for material transport and handling tasks in intelligent manufacturing systems