Proto-Plasm: parallel language for adaptive and scalable modelling of biosystems

This paper discusses the design goals and the first developments of Proto-Plasm, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the Proto-Plasm platform is still in its infancy. Its computational framework—language, model library, integrated development environment and parallel engine—intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. Proto-Plasm may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a Proto-Plasm program. Here we exemplify the basic functionalities of Proto-Plasm, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions

Progressive Transmission of Large Archaeological Models

Entrepreneurship motivation plays important role in developing new business organization. This research addresses to test variable influence entrepreneurship among students in East Java.  It refers to the theory of planned behavior  modified by Segel et. al (2004)  that uses three dependent variables, they are perceived feasibility or self afficacy (SE), risk tolerence (TR) and net desirability of self employment (NDSE) to explain entreprenuership motivation.To test this assertions, sample used are 854 students from 10 universities in Surabaya, Malang and Jember. Then, hypothesis both partial and simultanious  variables, SE,TR and NDSE have positive relation to entrepreneurship motivation (MB) tested by regression and correlation analysis. As a result,  findings support hypotesis and have significant implication for the way in which we conceptualize entrepreneurship motivation

Human perception-oriented segmentation for triangle meshes

A segmentação de malhas é um tópico importante de investigação em computação gráfica, em particular em modelação geométrica. Isto deve-se ao facto de as técnicas de segmentaçãodemalhasteremváriasaplicações,nomeadamentenaproduçãodefilmes, animaçãoporcomputador, realidadevirtual, compressãodemalhas, assimcomoemjogosdigitais. Emconcreto, asmalhastriangularessãoamplamenteusadasemaplicações interativas, visto que sua segmentação em partes significativas (também designada por segmentação significativa, segmentação perceptiva ou segmentação perceptualmente significativa ) é muitas vezes vista como uma forma de acelerar a interação com o utilizador ou a deteção de colisões entre esses objetos 3D definidos por uma malha, bem como animar uma ou mais partes significativas (por exemplo, a cabeça de uma personagem) de um dado objeto, independentemente das restantes partes. Acontece que não se conhece nenhuma técnica capaz de segmentar correctamente malhas arbitrárias −ainda que restritas aos domínios de formas livres e não-livres− em partes significativas. Algumas técnicas são mais adequadas para objetos de forma não-livre (por exemplo, peças mecânicas definidas geometricamente por quádricas), enquanto outras são mais talhadas para o domínio dos objectos de forma livre. Só na literatura recente surgem umas poucas técnicas que se aplicam a todo o universo de objetos de forma livre e não-livre. Pior ainda é o facto de que a maioria das técnicas de segmentação não serem totalmente automáticas, no sentido de que quase todas elas exigem algum tipo de pré-requisitos e assistência do utilizador. Resumindo, estes três desafios relacionados com a proximidade perceptual, generalidade e automação estão no cerne do trabalho descrito nesta tese. Para enfrentar estes desafios, esta tese introduz o primeiro algoritmo de segmentação baseada nos contornos ou fronteiras dos segmentos, cuja técnica se inspira nas técnicas de segmentação baseada em arestas, tão comuns em análise e processamento de imagem,porcontraposiçãoàstécnicasesegmentaçãobaseadaemregiões. Aideiaprincipal é a de encontrar em primeiro lugar a fronteira de cada região para, em seguida, identificar e agrupar todos os seus triângulos internos. As regiões da malha encontradas correspondem a saliências e reentrâncias, que não precisam de ser estritamente convexas, nem estritamente côncavas, respectivamente. Estas regiões, designadas regiões relaxadamenteconvexas(ousaliências)eregiõesrelaxadamentecôncavas(oureentrâncias), produzem segmentações que são menos sensíveis ao ruído e, ao mesmo tempo, são mais intuitivas do ponto de vista da perceção humana; por isso, é designada por segmentação orientada à perceção humana (ou, human perception- oriented (HPO), do inglês). Além disso, e ao contrário do atual estado-da-arte da segmentação de malhas, a existência destas regiões relaxadas torna o algoritmo capaz de segmentar de maneira bastante plausível tanto objectos de forma não-livre como objectos de forma livre. Nesta tese, enfrentou-se também um quarto desafio, que está relacionado com a fusão de segmentação e multi-resolução de malhas. Em boa verdade, já existe na literatura uma variedade grande de técnicas de segmentação, bem como um número significativo de técnicas de multi-resolução, para malhas triangulares. No entanto, não é assim tão comum encontrar estruturas de dados e algoritmos que façam a fusão ou a simbiose destes dois conceitos, multi-resolução e segmentação, num único esquema multi-resolução que sirva os propósitos das aplicações que lidam com malhas simples e segmentadas, sendo que neste contexto se entende que uma malha simples é uma malha com um único segmento. Sendo assim, nesta tese descreve-se um novo esquema (entenda-seestruturasdedadosealgoritmos)demulti-resoluçãoesegmentação,designado por extended Ghost Cell (xGC). Este esquema preserva a forma das malhas, tanto em termos globais como locais, ou seja, os segmentos da malha e as suas fronteiras, bem como os seus vincos e ápices são preservados, não importa o nível de resolução que usamos durante a/o simplificação/refinamento da malha. Além disso, ao contrário de outros esquemas de segmentação, tornou-se possível ter segmentos adjacentes com dois ou mais níveis de resolução de diferença. Isto é particularmente útil em animação por computador, compressão e transmissão de malhas, operações de modelação geométrica, visualização científica e computação gráfica. Em suma, esta tese apresenta um esquema genérico, automático, e orientado à percepção humana, que torna possível a simbiose dos conceitos de segmentação e multiresolução de malhas trianguladas que sejam representativas de objectos 3D.The mesh segmentation is an important topic in computer graphics, in particular in geometric computing. This is so because mesh segmentation techniques find many applications in movies, computer animation, virtual reality, mesh compression, and games. Infact, trianglemeshesarewidelyusedininteractiveapplications, sothattheir segmentation in meaningful parts (i.e., human-perceptually segmentation, perceptive segmentationormeaningfulsegmentation)isoftenseenasawayofspeedinguptheuser interaction, detecting collisions between these mesh-covered objects in a 3D scene, as well as animating one or more meaningful parts (e.g., the head of a humanoid) independently of the other parts of a given object. It happens that there is no known technique capable of correctly segmenting any mesh into meaningful parts. Some techniques are more adequate for non-freeform objects (e.g., quadricmechanicalparts), whileothersperformbetterinthedomainoffreeform objects. Only recently, some techniques have been developed for the entire universe of objects and shapes. Even worse it is the fact that most segmentation techniques are not entirely automated in the sense that almost all techniques require some sort of pre-requisites and user assistance. Summing up, these three challenges related to perceptual proximity, generality and automation are at the core of the work described in this thesis. In order to face these challenges, we have developed the first contour-based mesh segmentation algorithm that we may find in the literature, which is inspired in the edgebased segmentation techniques used in image analysis, as opposite to region-based segmentation techniques. Its leading idea is to firstly find the contour of each region, and then to identify and collect all of its inner triangles. The encountered mesh regions correspond to ups and downs, which do not need to be strictly convex nor strictly concave, respectively. These regions, called relaxedly convex regions (or saliences) and relaxedly concave regions (or recesses), produce segmentations that are less-sensitive to noise and, at the same time, are more intuitive from the human point of view; hence it is called human perception- oriented (HPO) segmentation. Besides, and unlike the current state-of-the-art in mesh segmentation, the existence of these relaxed regions makes the algorithm suited to both non-freeform and freeform objects. In this thesis, we have also tackled a fourth challenge, which is related with the fusion of mesh segmentation and multi-resolution. Truly speaking, a plethora of segmentation techniques, as well as a number of multiresolution techniques, for triangle meshes already exist in the literature. However, it is not so common to find algorithms and data structures that fuse these two concepts, multiresolution and segmentation, into a symbiotic multi-resolution scheme for both plain and segmented meshes, in which a plainmeshisunderstoodasameshwithasinglesegment. So, weintroducesuchanovel multiresolution segmentation scheme, called extended Ghost Cell (xGC) scheme. This scheme preserves the shape of the meshes in both global and local terms, i.e., mesh segments and their boundaries, as well as creases and apices are preserved, no matter the level of resolution we use for simplification/refinement of the mesh. Moreover, unlike other segmentation schemes, it was made possible to have adjacent segments with two or more resolution levels of difference. This is particularly useful in computer animation, mesh compression and transmission, geometric computing, scientific visualization, and computer graphics. In short, this thesis presents a fully automatic, general, and human perception-oriented scheme that symbiotically integrates the concepts of mesh segmentation and multiresolution

High-Quality Simplification and Repair of Polygonal Models

Because of the rapid evolution of 3D acquisition and modelling methods, highly complex and detailed polygonal models with constantly increasing polygon count are used as three-dimensional geometric representations of objects in computer graphics and engineering applications. The fact that this particular representation is arguably the most widespread one is due to its simplicity, flexibility and rendering support by 3D graphics hardware. Polygonal models are used for rendering of objects in a broad range of disciplines like medical imaging, scientific visualization, computer aided design, film industry, etc. The handling of huge scenes composed of these high-resolution models rapidly approaches the computational capabilities of any graphics accelerator. In order to be able to cope with the complexity and to build level-of-detail representations, concentrated efforts were dedicated in the recent years to the development of new mesh simplification methods that produce high-quality approximations of complex models by reducing the number of polygons used in the surface while keeping the overall shape, volume and boundaries preserved as much as possible. Many well-established methods and applications require "well-behaved" models as input. Degenerate or incorectly oriented faces, T-joints, cracks and holes are just a few of the possible degenaracies that are often disallowed by various algorithms. Unfortunately, it is all too common to find polygonal models that contain, due to incorrect modelling or acquisition, such artefacts. Applications that may require "clean" models include finite element analysis, surface smoothing, model simplification, stereo lithography. Mesh repair is the task of removing artefacts from a polygonal model in order to produce an output model that is suitable for further processing by methods and applications that have certain quality requirements on their input. This thesis introduces a set of new algorithms that address several particular aspects of mesh repair and mesh simplification. One of the two mesh repair methods is dealing with the inconsistency of normal orientation, while another one, removes the inconsistency of vertex connectivity. Of the three mesh simplification approaches presented here, the first one attempts to simplify polygonal models with the highest possible quality, the second, applies the developed technique to out-of-core simplification, and the third, prevents self-intersections of the model surface that can occur during mesh simplification

PHYSICS-AWARE MODEL SIMPLIFICATION FOR INTERACTIVE VIRTUAL ENVIRONMENTS

Rigid body simulation is an integral part of Virtual Environments (VE) for autonomous planning, training, and design tasks. The underlying physics-based simulation of VE must be accurate and computationally fast enough for the intended application, which unfortunately are conflicting requirements. Two ways to perform fast and high fidelity physics-based simulation are: (1) model simplification, and (2) parallel computation. Model simplification can be used to allow simulation at an interactive rate while introducing an acceptable level of error. Currently, manual model simplification is the most common way of performing simulation speedup but it is time consuming. Hence, in order to reduce the development time of VEs, automated model simplification is needed. The dissertation presents an automated model simplification approach based on geometric reasoning, spatial decomposition, and temporal coherence. Geometric reasoning is used to develop an accessibility based algorithm for removing portions of geometric models that do not play any role in rigid body to rigid body interaction simulation. Removing such inaccessible portions of the interacting rigid body models has no influence on the simulation accuracy but reduces computation time significantly. Spatial decomposition is used to develop a clustering algorithm that reduces the number of fluid pressure computations resulting in significant speedup of rigid body and fluid interaction simulation. Temporal coherence algorithm reuses the computed force values from rigid body to fluid interaction based on the coherence of fluid surrounding the rigid body. The simulations are further sped up by performing computing on graphics processing unit (GPU). The dissertation also presents the issues pertaining to the development of parallel algorithms for rigid body simulations both on multi-core processors and GPU. The developed algorithms have enabled real-time, high fidelity, six degrees of freedom, and time domain simulation of unmanned sea surface vehicles (USSV) and can be used for autonomous motion planning, tele-operation, and learning from demonstration applications

Inorganic Fullerene-like Nanoparticles and Inorganic Nanotubes

The subjects of the presented papers cover a wide range of challenges in the area of inorganic fullerene-like nanoparticles and nanotubes. However, it can include only a few comprehensive experimental and theoretical efforts, stepwise evaluating the rationalization of the synthesis, and elucidation of the stability, mechanical, electronic and adhesive properties of these nanostructures. We believe that this thematic issue can be helpful, not only for an advanced researcher to grasp the latest developments in this field, but also to permit a beginner to gain a deeper insight into the field of inorganic fullerene-like nanoparticles and nanotubes

Doctor of Philosophy

dissertationWhile boundary representations, such as nonuniform rational B-spline (NURBS) surfaces, have traditionally well served the needs of the modeling community, they have not seen widespread adoption among the wider engineering discipline. There is a common perception that NURBS are slow to evaluate and complex to implement. Whereas computer-aided design commonly deals with surfaces, the engineering community must deal with materials that have thickness. Traditional visualization techniques have avoided NURBS, and there has been little cross-talk between the rich spline approximation community and the larger engineering field. Recently there has been a strong desire to marry the modeling and analysis phases of the iterative design cycle, be it in car design, turbulent flow simulation around an airfoil, or lighting design. Research has demonstrated that employing a single representation throughout the cycle has key advantages. Furthermore, novel manufacturing techniques employing heterogeneous materials require the introduction of volumetric modeling representations. There is little question that fields such as scientific visualization and mechanical engineering could benefit from the powerful approximation properties of splines. In this dissertation, we remove several hurdles to the application of NURBS to problems in engineering and demonstrate how their unique properties can be leveraged to solve problems of interest

Digital Library Services for Three-Dimensional Models

With the growth in computing, storage and networking infrastructure, it is becoming increasingly feasible for multimedia professionals—such as graphic designers in commercial, manufacturing, scientific and entertainment areas—to work with 3D digital models of the objects with which they deal in their domain. Unfortunately most of these models exist in individual repositories, and are not accessible to geographically distributed professionals who are in need of them. Building an efficient digital library system presents a number of challenges. In particular, the following issues need to be addressed: (1) What is the best way of representing 3D models in a digital library, so that the searches can be done faster? (2) How to compress and deliver the 3D models to reduce the storage and bandwidth requirements? (3) How can we represent the user\u27s view on similarity between two objects? (4) What search types can be used to enhance the usability of the digital library and how can we implement these searches, what are the trade-offs? In this research, we have developed a digital library architecture for 3D models that addresses the above issues as well as other technical issues. We have developed a prototype for our 3D digital library (3DLIB) that supports compressed storage, along with retrieval of 3D models. The prototype also supports search and discovery services that are targeted for 3-D models. The key to 3DLIB is a representation of a 3D model that is based on “surface signatures”. This representation captures the shape information of any free-form surface and encodes it into a set of 2D images. We have developed a shape similarity search technique that uses the signature images to compare 3D models. One advantage of the proposed technique is that it works in the compressed domain, thus it eliminates the need for uncompressing in content-based search. Moreover, we have developed an efficient discovery service consisting of a multi-level hierarchical browsing service that enables users to navigate large sets of 3D models. To implement this targeted browsing (find an object that is similar to a given object in a large collection through browsing) we abstract a large set of 3D models to a small set of representative models (key models). The abstraction is based on shape similarity and uses specially tailored clustering techniques. The browsing service applies clustering recursively to limit the number of key models that a user views at any time. We have evaluated the performance of our digital library services using the Princeton Shape Benchmark (PSB) and it shows significantly better precision and recall, as compared to other approaches