Implicit functions provide a fundamental basis to model 3D objects, no matter they are rigid or d... more Implicit functions provide a fundamental basis to model 3D objects, no matter they are rigid or deformable, in computer graphics and geometric modeling. This paper introduces a new constructive scheme of implicitly-defined 3D objects based on products of implicit functions. This scheme is in contrast with popular approaches like blobbies, meta balls and soft objects, which rely on the sum of specific implicit functions to fit a 3D object to a set of spheres.
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.
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...
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.
Implicit functions provide a fundamental basis to model 3D objects, no matter they are rigid or d... more Implicit functions provide a fundamental basis to model 3D objects, no matter they are rigid or deformable, in computer graphics and geometric modeling. This paper introduces a new constructive scheme of implicitly-defined 3D objects based on products of implicit functions. This scheme is in contrast with popular approaches like blobbies, meta balls and soft objects, which rely on the sum of specific implicit functions to fit a 3D object to a set of spheres.
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.
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...
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.
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Papers by Adriano Raposo