IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Jan 17, 2015
DNA encodes the genetic information of most living beings, except viruses that use RNA. Unlike ot... more DNA encodes the genetic information of most living beings, except viruses that use RNA. Unlike other types of molecules, DNA is not usually described by its atomic structure being instead usually described by its base-pair sequence, i.e., the textual sequence of its subsidiary molecules known as nucleotides (adenine (A), cytosine (C), guanine (G) and thymine (T)). The three-dimensional assembling of DNA molecules based on its base-pair sequence has been, for decades, a topic of interest for many research groups all over the world. In this paper we survey the major methods found in the literature to assemble and visualize DNA molecules from their base-pair sequences. We divided these methods into three categories: predictive methods, adaptive methods, and thermodynamic methods. Predictive methods aim to predict a conformation of the DNA from its base pair sequence, while the goal of adaptive methods is to assemble DNA base-pairs sequences along previously known conformations, as need...
This paper explores the use of Technical Performance Indexes (TPIs) to assess the operational per... more This paper explores the use of Technical Performance Indexes (TPIs) to assess the operational performance of Water Distribution Networks (WDNs) and exemplifies its suitability to easily identify problematic zones. The paper also points out some problems associated with the existent TPIs and proposes new analysis tools to avoid these difficulties. These new analysis tools (such as state variable slack and constraint violation) are conjugated with the pressure-driven simulation model for illustration purposes, including operational performance assessment during pipe bursts or firefighting scenarios, and to identity and account for the " demand not satisfied " due to those events.
Continuation algorithms usually behave badly near to critical points of implicitly defined curves... more Continuation algorithms usually behave badly near to critical points of implicitly defined curves in R2R2, i.e., points at which at least one of the partial derivatives vanishes. Critical points include turning points, self-intersections, and isolated points. Another problem with this family of algorithms is their inability to render curves with multiple components because that requires finding first a seed point on each of them. This paper details an algorithm that resolves these two major problems in an elegant manner. In fact, it allows us not only to march along a curve even in the presence of critical points, but also to detect and render curves with multiple components using the theory of critical points.
ABSTRACT Navier-Stokes-based methods have been used in computer graphics to simulate liquids, esp... more ABSTRACT Navier-Stokes-based methods have been used in computer graphics to simulate liquids, especially water. These physically based methods are computationally intensive, and require rendering the water surface at each step of the simulation process. The rendering of water surfaces requires knowing which 3D grid cells are crossed by the water's surface, that is, tracking the surface across the cells is necessary. Solutions to water surface tracking and rendering problems exist in literature, but they are either too computationally intensive to be appropriate for real-time scenarios, as is the case of deformable implicit surfaces and ray-tracing, or too application-specific, as is the case of height-fields to simulate and render water mantles e.g., lakes and oceans. This paper proposes a novel solution to water surface tracking that does not compromise the overall simulation performance. This approach differs from previous solutions in that it directly classifies and annotates the density of each 3D grid cell as either water, air, or water-air i.e., water surface, opening the opportunity for easily reconstructing the water surface at an interactive frame rate.
ABSTRACT Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling mode... more ABSTRACT Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling model for sequences of DNA base pairs using nucleotides, instead of atoms, as building blocks of DNA molecules. This nucleotide-based model is more scalable than the traditional atomistic model, and has the advantage that easily adapts to any topological conformation of DNA. Interestingly, this model also allows the building of the molecular surface of the DNA, either partly or entirely, as needed for energy computations in molecular applications. Moreover, it allows us to grasp the DNA shape at different levels of shape composition: atom, nucleotide, and DNA macromolecule as a whole.
Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, partic... more Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods randomly generate a new trial conformation, which is either accepted or rejected according to a criterion based on energy calculations and stochastic rules. These simulation trials are generated using a method based on crankshaft motion that, apart from some slight improvements, has remained the same for many years. In this paper, we present a new algorithm for the deformation of plasmid DNA molecules for Monte Carlo simulations. The move underlying our algorithm preserves the size and connectivity of straight-line segments of the plasmid DNA skeleton. We also present the results of three experiments comparing our deformation move with the standard and biased crankshaft moves in terms of acceptance ratio of the trials, energy and temperature evolution, and average displacement of the molecule. Our algorithm can also be used as a generic geometric algorithm for the deformation of regular polygons or polylines that preserves the connections and lengths of their segments. Compared with both crankshaft moves, our move generates simulation trials with higher acceptance ratios and smoother deformations, making it suitable for real-time visualization of plasmid DNA coiling. For that purpose, we have adopted a DNA assembly algorithm that uses nucleotides as building blocks.
ABSTRACT Many zero-finding numerical methods are based on the Intermediate Value Theorem, which s... more ABSTRACT Many zero-finding numerical methods are based on the Intermediate Value Theorem, which states that a zero of a real function is bracketed in a given interval if and have opposite signs; that is, . But, some zeros cannot be bracketed this way because they do not satisfy the precondition . For example, local minima and maxima that annihilate may not be bracketed by the Intermediate Value Theorem. In this case, we can always use a numerical method for bracketing extrema, checking then whether it is a zero of or not. Instead, this paper introduces a single numerical method, called generalized regula falsi (GRF) method to determine both zeros and extrema of a function. Consequently, it differs from the standard regula falsi method in that it is capable of finding any function zero in a given interval even when the Intermediate Value Theorem is not satisfied.
Page 1. i jgt 2008/11/13 20:29 page 15 #1 i i i Vol. 13, No. 3: 1533 A Nonoriented, No... more Page 1. i jgt 2008/11/13 20:29 page 15 #1 i i i Vol. 13, No. 3: 1533 A Nonoriented, Nonmanifold Boundary Representation for Geometric Applications Frutuoso GM Silva and Abel JP Gomes University of Beira Interior Abstract. ...
Concurrency and Computation: Practice and Experience, 2011
Page 1. CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper.... more Page 1. CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. (2011) Published online in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/cpe.1783 SPECIAL ISSUE PAPER ...
Root-flnding numerical methods are based on the Intermediate Value Theorem. It states that a root... more Root-flnding numerical methods are based on the Intermediate Value Theorem. It states that a root of a real function f :R !R is bracketed in a given interval (A;B) ‰R if f(A) and f(B) have opposite signs, i.e. f(A):f(B) < 0. But, some roots cannot be bracketed this way because they do not satisfy the pre-condition f(A):f(B) < 0. For example, local minima and maxima that annihilate f may not be bracketed by the Inter- mediate Value Theorem. In this case, we can always use a numerical method for bracketing extrema, checking then whether it is a zero of f or not. Instead, this paper introduces a single numerical method, called generalized false position method (GFP) to determine both zeros and extrema of a function. Consequently, it difiers from the standard false position method in that it is capable of flnding any function zero in a given interval (A;B) ‰R even when the Intermediate Value Theorem is not satisfled. c ∞ 2008 European Society of Computational Methods in Sciences and Engineering
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Jan 17, 2015
DNA encodes the genetic information of most living beings, except viruses that use RNA. Unlike ot... more DNA encodes the genetic information of most living beings, except viruses that use RNA. Unlike other types of molecules, DNA is not usually described by its atomic structure being instead usually described by its base-pair sequence, i.e., the textual sequence of its subsidiary molecules known as nucleotides (adenine (A), cytosine (C), guanine (G) and thymine (T)). The three-dimensional assembling of DNA molecules based on its base-pair sequence has been, for decades, a topic of interest for many research groups all over the world. In this paper we survey the major methods found in the literature to assemble and visualize DNA molecules from their base-pair sequences. We divided these methods into three categories: predictive methods, adaptive methods, and thermodynamic methods. Predictive methods aim to predict a conformation of the DNA from its base pair sequence, while the goal of adaptive methods is to assemble DNA base-pairs sequences along previously known conformations, as need...
This paper explores the use of Technical Performance Indexes (TPIs) to assess the operational per... more This paper explores the use of Technical Performance Indexes (TPIs) to assess the operational performance of Water Distribution Networks (WDNs) and exemplifies its suitability to easily identify problematic zones. The paper also points out some problems associated with the existent TPIs and proposes new analysis tools to avoid these difficulties. These new analysis tools (such as state variable slack and constraint violation) are conjugated with the pressure-driven simulation model for illustration purposes, including operational performance assessment during pipe bursts or firefighting scenarios, and to identity and account for the " demand not satisfied " due to those events.
Continuation algorithms usually behave badly near to critical points of implicitly defined curves... more Continuation algorithms usually behave badly near to critical points of implicitly defined curves in R2R2, i.e., points at which at least one of the partial derivatives vanishes. Critical points include turning points, self-intersections, and isolated points. Another problem with this family of algorithms is their inability to render curves with multiple components because that requires finding first a seed point on each of them. This paper details an algorithm that resolves these two major problems in an elegant manner. In fact, it allows us not only to march along a curve even in the presence of critical points, but also to detect and render curves with multiple components using the theory of critical points.
ABSTRACT Navier-Stokes-based methods have been used in computer graphics to simulate liquids, esp... more ABSTRACT Navier-Stokes-based methods have been used in computer graphics to simulate liquids, especially water. These physically based methods are computationally intensive, and require rendering the water surface at each step of the simulation process. The rendering of water surfaces requires knowing which 3D grid cells are crossed by the water's surface, that is, tracking the surface across the cells is necessary. Solutions to water surface tracking and rendering problems exist in literature, but they are either too computationally intensive to be appropriate for real-time scenarios, as is the case of deformable implicit surfaces and ray-tracing, or too application-specific, as is the case of height-fields to simulate and render water mantles e.g., lakes and oceans. This paper proposes a novel solution to water surface tracking that does not compromise the overall simulation performance. This approach differs from previous solutions in that it directly classifies and annotates the density of each 3D grid cell as either water, air, or water-air i.e., water surface, opening the opportunity for easily reconstructing the water surface at an interactive frame rate.
ABSTRACT Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling mode... more ABSTRACT Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling model for sequences of DNA base pairs using nucleotides, instead of atoms, as building blocks of DNA molecules. This nucleotide-based model is more scalable than the traditional atomistic model, and has the advantage that easily adapts to any topological conformation of DNA. Interestingly, this model also allows the building of the molecular surface of the DNA, either partly or entirely, as needed for energy computations in molecular applications. Moreover, it allows us to grasp the DNA shape at different levels of shape composition: atom, nucleotide, and DNA macromolecule as a whole.
Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, partic... more Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods randomly generate a new trial conformation, which is either accepted or rejected according to a criterion based on energy calculations and stochastic rules. These simulation trials are generated using a method based on crankshaft motion that, apart from some slight improvements, has remained the same for many years. In this paper, we present a new algorithm for the deformation of plasmid DNA molecules for Monte Carlo simulations. The move underlying our algorithm preserves the size and connectivity of straight-line segments of the plasmid DNA skeleton. We also present the results of three experiments comparing our deformation move with the standard and biased crankshaft moves in terms of acceptance ratio of the trials, energy and temperature evolution, and average displacement of the molecule. Our algorithm can also be used as a generic geometric algorithm for the deformation of regular polygons or polylines that preserves the connections and lengths of their segments. Compared with both crankshaft moves, our move generates simulation trials with higher acceptance ratios and smoother deformations, making it suitable for real-time visualization of plasmid DNA coiling. For that purpose, we have adopted a DNA assembly algorithm that uses nucleotides as building blocks.
ABSTRACT Many zero-finding numerical methods are based on the Intermediate Value Theorem, which s... more ABSTRACT Many zero-finding numerical methods are based on the Intermediate Value Theorem, which states that a zero of a real function is bracketed in a given interval if and have opposite signs; that is, . But, some zeros cannot be bracketed this way because they do not satisfy the precondition . For example, local minima and maxima that annihilate may not be bracketed by the Intermediate Value Theorem. In this case, we can always use a numerical method for bracketing extrema, checking then whether it is a zero of or not. Instead, this paper introduces a single numerical method, called generalized regula falsi (GRF) method to determine both zeros and extrema of a function. Consequently, it differs from the standard regula falsi method in that it is capable of finding any function zero in a given interval even when the Intermediate Value Theorem is not satisfied.
Page 1. i jgt 2008/11/13 20:29 page 15 #1 i i i Vol. 13, No. 3: 1533 A Nonoriented, No... more Page 1. i jgt 2008/11/13 20:29 page 15 #1 i i i Vol. 13, No. 3: 1533 A Nonoriented, Nonmanifold Boundary Representation for Geometric Applications Frutuoso GM Silva and Abel JP Gomes University of Beira Interior Abstract. ...
Concurrency and Computation: Practice and Experience, 2011
Page 1. CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper.... more Page 1. CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. (2011) Published online in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/cpe.1783 SPECIAL ISSUE PAPER ...
Root-flnding numerical methods are based on the Intermediate Value Theorem. It states that a root... more Root-flnding numerical methods are based on the Intermediate Value Theorem. It states that a root of a real function f :R !R is bracketed in a given interval (A;B) ‰R if f(A) and f(B) have opposite signs, i.e. f(A):f(B) < 0. But, some roots cannot be bracketed this way because they do not satisfy the pre-condition f(A):f(B) < 0. For example, local minima and maxima that annihilate f may not be bracketed by the Inter- mediate Value Theorem. In this case, we can always use a numerical method for bracketing extrema, checking then whether it is a zero of f or not. Instead, this paper introduces a single numerical method, called generalized false position method (GFP) to determine both zeros and extrema of a function. Consequently, it difiers from the standard false position method in that it is capable of flnding any function zero in a given interval (A;B) ‰R even when the Intermediate Value Theorem is not satisfled. c ∞ 2008 European Society of Computational Methods in Sciences and Engineering
Implicit objects have gained increasing importance in geometric modeling, visualisation, animatio... more Implicit objects have gained increasing importance in geometric modeling, visualisation, animation, and computer graphics, because their geometric properties provide a good alternative to traditional parametric objects. This book presents the mathematics, computational methods and data structures, as well as the algorithms needed to render implicit curves and surfaces, and shows how implicit objects can easily describe smooth, intricate, and articulatable shapes, and hence why they are being increasingly used in ...
Several fields of mathematics are relevant to computer aided design and other software systems in... more Several fields of mathematics are relevant to computer aided design and other software systems involving solid object geometry, topology, dif-ferential and algebraic geometry being particularly important. This paper discusses some of this mathematics in order to provide a theoretical foun-dation for geometric modelling kernels that support non-manifold objects with an internal cellular structure and subsets of different dimensions. The paper shows relationships between relevant concepts from topol-ogy, differential geometry and computer aided geometric design that are not widely known in the CAD community. It also discusses semialgebraic, semianalytic and subanalytic sets as candidates for object representation. Stratifications of such sets are proposed for an object's cellular structure and new stratification concepts are introduced to support candidate ap-plications. Acknowledgements This paper was motivated by the Djinn research project funded by the Engineering and Physical ...
Abstract Form features have been around since early 80's. However, until recently, n... more Abstract Form features have been around since early 80's. However, until recently, no (mathematical) theory underpinning form feature-based modelling has been proposed. This is largely because of an incomplete understanding of the relationships between shape ...
EPANEt extension for synthetic Water Distribution Networks generation and sizing. Simulation dema... more EPANEt extension for synthetic Water Distribution Networks generation and sizing. Simulation deman-driven and pressure-driven. Leakage simulation. Performance evaluation.
The color is a very important asset when comes the time of interacting with other people and the ... more The color is a very important asset when comes the time of interacting with other people and the ambient world, where the color may turn into the message itself. As known, about 5% of the people all over the world suffer from colorblindness, also formally called color vision deficit (CVD). It is clear that this visual impairment compromises the way those people see and interpret their surroundings and the visual messages they receive continuously. This is particularly relevant not only for those who need to correctly interpret the traffic lights — and recall that color blind because people see reds and greens in the same way —, but also for those who use the web for leisure and professional purposes daily. With this critical problem in mind, this paper proposes a new algorithm to adjust those colors that shed confusion on dichromate people (deuteranopes and protanopes). This algorithm takes advantage of a simple formula that operates on the HSV color space. The implementation of the...
Proceedings Computer Graphics International 2003, 2003
Page 1. Interactive Editing of Arbitrary Sub-meshes Frutuoso GM Silva and Abel JP Gomes IT - Netw... more Page 1. Interactive Editing of Arbitrary Sub-meshes Frutuoso GM Silva and Abel JP Gomes IT - Networks and Multimedia Group University of Beira Interior {fsilva, agomes}@di.ubi.pt Abstract This paper presents a novel approach ...
Meshing is an important topic in geometric modelling and computer graphics. This paper introduces... more Meshing is an important topic in geometric modelling and computer graphics. This paper introduces a concise and fast data structure, called AIF (Adjacency and Incidence Framework). Its conciseness results from the fact that it is an orientable, but not an oriented, data structure, i.e. an orientation can be topologically induced as necessary in many applications. It is an optimal C
Abstract. Traditionally, B-rep geometric kernels possess oriented data structures, ie they posses... more Abstract. Traditionally, B-rep geometric kernels possess oriented data structures, ie they possess oriented cells (eg half-edges, co-edges, face uses, etc.). The use of explicit oriented cells makes these data structures quite verbose and expensive in terms of memory space. Although ...
Abstract. Multiresolution meshes enable us to build representations of geometric objects at diffe... more Abstract. Multiresolution meshes enable us to build representations of geometric objects at different Levels of Detail (LODs). We introduce a multiresolution scheme whose data structure allows us to separately re-store the geometry and topology of a mesh during the refinement ...
Proceedings - Theory and Practice of Computer Graphics 2004, 2004
Page 1. Normal-based simplification algorithm for meshes Frutuoso GM Silva and Abel JP Gomes IT -... more Page 1. Normal-based simplification algorithm for meshes Frutuoso GM Silva and Abel JP Gomes IT - Networks and Multimedia Group Department of Computer Science and Engineering University of Beira Interior - Portugal {fsilva, agomes}@di.ubi.pt Abstract ...
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2010
AbstractThe problem addressed in this paper consists in triangulating the van der Waals surface ... more AbstractThe problem addressed in this paper consists in triangulating the van der Waals surface without computing the geometric intersections of its atoms. Recall that the van der Waals surface is useful in computational molecular biology and biochemistry to, for example, determine ...
Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13, 2013
ABSTRACT Current GPU-based workstations are inadequate to triangulate and rendering large molecul... more ABSTRACT Current GPU-based workstations are inadequate to triangulate and rendering large molecular datasets with thousands and hundreds of thousands, not to say millions, of atoms. The problem is not so the lack of processing power, but the memory limitations of current GPU graphics cards. For example, the NVidia GeForce GTX 590 graphics card comes with two 1.5GB GPUs. We tackle here this problem using a OpenMP-CUDA solution that runs on a loosely-coupled GPU cluster. Basically, we propose a fast, scalable, parallel triangulation algorithm for molecular surfaces that takes advantage of multicore processors of CPUs and GPUs of modern hardware architectures, where each CPU core works as the master of a single GPU, being the processing burden distributed over the CPU cores available in a single computer or a cluster. As much as we know, this is the first marching cubes algorithm that triangulates molecular surfaces on multiple GPUs using CUDA and OpenMP.
We propose a new pathfinding technique called xTrek that combines conventional pathfinding and in... more We propose a new pathfinding technique called xTrek that combines conventional pathfinding and influence fields; that is, we are introducing a new influence-sensitive pathfinder or influence-aware pathfinder. The leading idea of influence-aware pathfinding is to avoid unwanted regions and/or converge to desired regions of the search space during the path search. As shown throughout the paper, this region avoidance/convergence is more striking using our technique than in other field-aware pathfinders as, for example, risk-adverse pathfinders and constraint-aware navigation pathfinders. Furthermore, our technique constrains the search space even more than such state-of-the-art influence-aware pathfinders, aiming to reduce the memory space consumption, to speed up pathfinding computations, and at the same time to have better control on the paths to be discovered.
Piecewise linear curves, also known as polylines, are often used in computer graphics as approxim... more Piecewise linear curves, also known as polylines, are often used in computer graphics as approximations to three-dimensional curves to model arbitrarily deformable string-like objects. Most of the existing methods used to deform piecewise linear curves do not preserve the number and length of the edges. In this paper, we present a new geometric method to perform arbitrary deformation of three-dimensional piecewise linear curves, open or closed, preserving the length of the edges. The paper divides the curves into two categories: piecewise linear curves with equally-sized edges and piecewise linear curves with unequally-sized edges. In this sense, the paper presents a deformation algorithm for piecewise linear curves with equally-sized edges and its generalization for piecewise linear curves with unequally-sized edges. Also, one considers the particular case of deformation of regular polygons, often used in applications as, for example, closed-circular DNA molecular simulations.
IEEE Transactions on Computational Intelligence and AI in Games, 2017
In virtual worlds (including computer games), users develop trust relationships from their in-wor... more In virtual worlds (including computer games), users develop trust relationships from their in-world interactions with others. However, these trust relationships end up not being represented in the data structures (or databases) of such virtual worlds, though they sometimes appear associated with reputation and recommendation systems. In addition, as far as we know, the user is not provided with a personal trust tool to sustain his/her decision-making while he/she interacts with other users in the virtual or game world. In order to come up with a computational formal representation of these personal trust relationships, we need to succeed in converting in-world interactions into reliable sources of trust-related data. In this paper, we develop the required formalisms to gather and represent in-world interactions—which are based on the activity theory—as well as a method to convert in-world interactions into trust networks. In the companion paper, we use these trust networks to produce a computational trust decision based on subjective logic. This solution aims at supporting in-world user (or avatar) decisions about others in the game world.
ABSTRACT This paper introduces a concise and responsiveness data structure, called AIF (Adjacency... more ABSTRACT This paper introduces a concise and responsiveness data structure, called AIF (Adjacency and Incidence Framework), for multiresolution meshes, as well as a new simplification algorithm based on the planarity of neighboring faces. It is an optimal data structure for polygonal meshes, manifold and non-manifold, which means that a minimal number of direct and indirect accesses are required to retrieve adjacency and incidence information from it. These querying tools are necessary for dynamic multiresolution meshing algorithms (e.g. refinement and simplification operations). AIF is an orientable, but not oriented, data structure, i.e. an orientation can be topologically induced as needed in many computer graphics and geometric modelling applications. On the other hand, the simplification algorithm proposed in this paper is "memoryless" in the sense that only the current approximation counts to compute the next one; no information about the original shape or previous approximations is considered.
Resumo Este artigo introduz uma nova estrutura de dados b-rep (boundary representation) designada... more Resumo Este artigo introduz uma nova estrutura de dados b-rep (boundary representation) designada de AIF (Adjacency and Incidence Framework). A estrutura de dados AIF é concisa e permite o acesso rápido à sua informação topológica. A sua concisão resulta do facto de ser uma estrutura de dados orientável mas não orientada, isto é, a orientação é induzida topologicamente como é necessário em várias aplicações. É uma estrutura de dados óptima na classe 9 4 C , o que significa que um número mínimo de acessos é necessário para aceder a toda a informação sobre adjacências e incidências. A estrutura de dados AIF suporta a representação de modelos poligonais, não necessariamente triangulares, mesmo em condições de “ non-manifold” .
ABSTRACT Navier-Stokes-based methods have been used in computer graphics to simulate liquids, esp... more ABSTRACT Navier-Stokes-based methods have been used in computer graphics to simulate liquids, especially water. These physically based methods are computationally intensive, and require rendering the water surface at each step of the simulation process. The rendering of water surfaces requires knowing which 3D grid cells are crossed by the water's surface, that is, tracking the surface across the cells is necessary. Solutions to water surface tracking and rendering problems exist in literature, but they are either too computationally intensive to be appropriate for real-time scenarios, as is the case of deformable implicit surfaces and ray-tracing, or too application-specific, as is the case of height-fields to simulate and render water mantles e.g., lakes and oceans. This paper proposes a novel solution to water surface tracking that does not compromise the overall simulation performance. This approach differs from previous solutions in that it directly classifies and annotates the density of each 3D grid cell as either water, air, or water-air i.e., water surface, opening the opportunity for easily reconstructing the water surface at an interactive frame rate.
CavBench's protein cavity datasets, which include cavities output by the following cavity det... more CavBench's protein cavity datasets, which include cavities output by the following cavity detection methods: Fpocket, KVFinder, GHECOM, and Gaussian Finder. It is clear that ground truth dataset of protein cavities is also included.
Re-engineering Jake2 (Quake2 port to Java) to work on a grid is not a trivial task. For that purp... more Re-engineering Jake2 (Quake2 port to Java) to work on a grid is not a trivial task. For that purpose, we had to migrate a networking client-server model to a grid-based model. Networking games is an area where considerable computational gains might be obtained using this migration, in particular management and optimization of resources (i.e. processor and memory usage).
Virtual Reality has become an important educational tool, due to the pandemic and increasing glob... more Virtual Reality has become an important educational tool, due to the pandemic and increasing globalization of education. In this paper, we present a framework for teaching Virtual Anatomy at the university level. Because of the isolation and quarantine requirements and the increased international collaboration, virtual classes have become a staple of today’s curricula. Our work builds on the Visible Human Projects for Virtual Dissection material and provides a medium for groups of students to do collaborative anatomical dissections in real-time using sketching and 3D visualizations and audio coupled with interactive 2D tablets for precise drawing. We describe the system architecture, compare requirements with those of a previous development [1] and discuss the preliminary results. Discussions with Anatomists show that this is an effective tool. We introduce avenues for further research and discuss collaboration challenges posed by this context.
A reconstrução de uma superfície triangulada a partir de uma nuvem de pontos é um problema difíci... more A reconstrução de uma superfície triangulada a partir de uma nuvem de pontos é um problema difícil de resolver dado depender da forma do objeto original e da densidade dos pontos obtidos pelo dispositivo de aquisição 3D utilizado (scanner). Em grande medida, os algoritmos baseados em expansão da malha que existem na literatura não são bem-sucedidos porque os triângulos são apensos à malha em expansão com base em intervalos angulares que não podem ser ultrapassados. Por contraposição, propõe-se neste artigo um algoritmo que resolve este problema através da conjunção de funções que quantificam três propriedades geométricas fundamentais: coplanaridade, proximidade e regularidade.
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Journal Papers by Abel Gomes