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- Multi-GPU-Based Detection of Protein Cavities using Critical PointsPublication . Dias, Sérgio; Nguyen, Quoc; Jorge, Joaquim A; Gomes, AbelProtein cavities are specific regions on the protein surface where ligands (small molecules) may bind. Such cavities are putative binding sites of proteins for ligands. Usually, cavities correspond to voids, pockets, and depressions of molecular surfaces. The location of such cavities is important to better understand protein functions, as needed in, for example, structure-based drug design. This article introduces a geometric method to detecting cavities on the molecular surface based on the theory of critical points. The method, called CriticalFinder, differs from other surface-based methods found in the literature because it directly uses the curvature of the scalar field (or function) that represents the molecular surface, instead of evaluating the curvature of the Connolly function over the molecular surface. To evaluate the accuracy of CriticalFinder, we compare it to other seven geometric methods (i.e., LIGSITE-CS, GHECOM, ConCavity, POCASA, SURFNET, PASS, and Fpocket). The benchmark results show that CriticalFinder outperforms those methods in terms of accuracy. In addition, the performance analysis of the GPU implementation of CriticalFinder in terms of time consumption and memory space occupancy was carried out.
- Contour Enhancement Algorithm for Improving Visual Perception of Deutan and Protan DichromatsPublication . Ribeiro, Madalena; Gomes, AbelA variety of recoloring methods has been proposed in the literature to remedy the problem of confusing red-green colors faced by dichromat people (as well by other color-blinded people). The common strategy to mitigate this problem is to remap colors to other colors. But, it is clear this does not guarantee neither the necessary contrast to distinguish the elements of an image, nor the naturalness of colors learnt from past experience of each individual. In other words, the individual’s perceptual learning may not hold under color remapping. With this in mind, we introduce the first algorithm primarily focused on the enhancement of object contours in still images, instead of recoloring the pixels of the regions bounded by such contours. This is particularly adequate to increase contrast in images where we find adjacent regions that are color-indistinguishable from the dichromacy’s point of view.
- A gyro-enhanced smart-phone framework to develop motion-based user interfaces for animation and virtual environmentsPublication . Pereira, Tiago; Pereira, Orlando; Fazendeiro, Paulo; Gomes, AbelIn this paper, the mobile phone is presented as an alternative device to interact with animation systems and virtual environments, including video games. Basically, we show how the gyroscope of a mobile device can work as a sensor to control the pose and motion of a mobile device controlled object or character in a 3D virtual world. More specifically, we introduce a framework that enables the development and rapid prototyping of motion-based user interfaces for animation systems and virtual environments. This framework provides tools to capture and control the motion of mobile devices-binded objects in a 3D virtual scene over a wireless communication channel via a simple, fast and efficient protocol named Open Sound Control (OSC).
- A User Trust System for Online Games: Part IPublication . Cardoso, Rui Costa; Freire, Mario; Gomes, AbelIn 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.
- Real-Time Simulation of Cumulus Clouds through SkewT/LogP DiagramsPublication . Duarte, Rui; Gomes, AbelModeling, simulation, and realistic rendering of natural phenomena have been important goals in computer graphics for decades. Clouds, as a natural phenomenon, represent a real challenge because their birth, life, and death are amorphous and dynamic in nature. As a consequence, cloud simulation is very time-consuming when using physically-based methods. This paper presents a real-time cloud simulation method based on SkewT/LogP diagrams to overcome this time performance problem. These diagrams allow us to simulate 3D clouds from sounding data made public worldwide by weather agencies. More specifically, a SkewT/LogP diagram describes the vertical motion of a cloud in the atmosphere, i.e., our cloud simulator system is based on physics but avoids solving differential equations of cloud motion to achieve real-time rates. We have also built a visual tool for 2D SkewT/LogP diagrams that allows us to inspect, control and simulate the thermodynamic process of ascending clouds in the atmosphere, as well as a 3D synthetic environment where clouds are advected by buoyant forces. This lightweight physically-based technique enables the incorporation of our cloud simulator in systems tied to important industries, namely movies, virtual environments, and video games.
- Recoloring Algorithms for Colorblind People: A SurveyPublication . Ribeiro, Madalena; Gomes, AbelColor is a powerful communication component, not only as part of the message meaning but also as a way of discriminating contents therein. However, 5% of the world’s population suffers from color vision deficiency (CVD), commonly known as colorblindness. This handicap adulterates the way the color is perceived, compromising the reading and understanding of the message contents. This issue becomes even more pertinent due to the increasing availability of multimedia contents in computational environments (e.g., web browsers). Aware of this problem, a significant number of CVD research works came up in the literature in the past two decades to improve color perception in text documents, still images, video, and so forth. This survey mainly addresses recoloring algorithms toward still images for colorblind people, including the current trends in the field of color adaptation.
- Part-based Mesh Segmentation: a SurveyPublication . Rodrigues, Rui Sérgio Viegas; Morgado, José; Gomes, AbelThis paper surveys mesh segmentation techniques and algorithms, with a focus on part‐based segmentation, that is, segmentation that divides a mesh (featuring a 3D object) into meaningful parts. Part‐based segmentation applies to a single object and also to a family of objects (i.e. co‐segmentation). However, we shall not address here chart‐based segmentation, though some mesh co‐segmentation methods employ such chart‐based segmentation in the initial step of their pipeline. Finally, the taxonomy proposed in this paper is new in the sense that one classifies each segmentation algorithm regarding the dimension (i.e. 1D, 2D and 3D) of the representation of object parts. The leading idea behind this survey is to identify the properties and limitations of the state‐of‐the‐art algorithms to shed light on the challenges for future work.
- GPU-Based De- tection of Protein Cavities using Gaussian SurfacesPublication . Dias, Sérgio; Martins, Ana Mafalda; Nguyen, Quoc; Gomes, AbelProtein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. Also, it is hard to distinguish grid nodes belonging to protein cavities amongst all those outside the protein, a problem that we call cavity ceiling ambiguity.
- Calibration in Water Distribution Networks with Pressure-Driven AnalysisPublication . Muranho, João; Ferreira, Ana; Gomes, Abel; Sousa, J.; Marques, Alfeu SáWater distribution networks (WDN) connect consumers to the water sources, and its goal is to fulfil water demand. However, it is a well-known fact that WDN have losses and an important part of them occur at pipe level. Despite all the research efforts focused on this subject, the identification of leaky pipes is still a major challenge. EPANET is frequently used to simulate WDN’ models, using a link-node formulation, similar to a graph, where the water demands are assigned to the nodes. A linearized system of equations (mass and energy conservation laws) is iteratively solved by a Newton-Raphson algorithm. The EPANET is demand-driven, since it assumes the water pressure is always enough to satisfy the demands. However, on real WDN, states of insufficient pressure also occur. Besides that, the demand-driven approach is not suitable for pipe leakage simulation, which depends on the pressure. WaterNetGen — an EPANET extension— allows both demand and pressure driven simulations, including pipes’ leakage modelling. However, the leakage parameters (bursts and background leakage coefficients and exponents) must be set manually by an expert — manual calibration — for the whole network or for each pipe. This work proposes a calibration methodology to estimate the pipe background leakage parameters. The approach is tested on a set of synthetic models, generated by WaterNetGen, and then applied to a real WDN to assess its performance on real world conditions.
- Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A SurveyPublication . Simões, Tiago M. C.; Lopes, Daniel Simões; Dias, Sérgio Emanuel Duarte; Fernandes, Francisco; Jorge, Joaquim A; Pereira, João; Bajaj, Chandrajit; Gomes, AbelDetecting and analysing protein cavities provides significant information about active sites for biological processes (e.g. protein–protein or protein–ligand binding) in molecular graphics and modelling. Using the three‐dimensional (3D) structure of a given protein (i.e. atom types and their locations in 3D) as retrieved from a PDB (Protein Data Bank) file, it is now computationally viable to determine a description of these cavities. Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels and grooves on the surface of a given protein. In this work, we survey the literature on protein cavity computation and classify algorithmic approaches into three categories: evolution‐based, energy‐based and geometry‐based. Our survey focuses on geometric algorithms, whose taxonomy is extended to include not only sphere‐, grid‐ and tessellation‐based methods, but also surface‐based, hybrid geometric, consensus and time‐varying methods. Finally, we detail those techniques that have been customized for GPU (graphics processing unit) computing.