Mathematical generalization from the articulation of advanced mathematical thinking and knot theory

Background: The professors of Topology and modern algebra expressed interest in the need to create a space that allows deepening the process of Mathematical Generalization from the articulation of some concepts of Theory of Knots with the development of Advanced Mathematical Thinking (PMA) skills. Objective: To offer students an additional space for disciplinary training that allows them to deepen the process of Mathematical Generalization. Design: The methodology used has a qualitative approach, as a strategy we take action research from the Whitehead (1991) proposal from three phases. Setting and participants: students of the Bachelor of Mathematics program who take the third to sixth semester. Data collection and analysis: we emphasized in the second phase (intervention), since it allowed us to articulate the holistic scheme of knot theory with the PMA as shown in Tables 2, 3 and 4 (results section). Results: The result was the creation of a syllabus and subject guide for an elective seminar, which is offered to undergraduate students. Conclusion: since 2019 this elective seminar is offered to students, which awards 3 credits

Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids

In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins

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

Monte Carlo implementation of supercoiled double-stranded DNA

Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending constrained by hydrogen bonds formed between DNA complementary nucleotide bases. Three evident regimes are found in extension versus torsion and/or force versus extension plots: a low-force regime in which over- and underwound molecules behave similarly under stretching; an intermediate-force regime in which chirality appears for negatively and positively supercoiled DNA and extension of underwound molecule is insensitive to the supercoiling degree of the polymer; and a large-force regime in which plectonemic DNA is fully converted to extended DNA and supercoiled DNA behaves quite like a torsionless molecule. The striking coincidence between theoretic calculations and recent experimental measurement of torsionally stretched DNA [Strick et al., Science {\bf 271}, 1835 (1996), Biophys. J. {\bf 74}, 2016 (1998)] strongly suggests that the interplay between base-stacking interaction and permanent hydrogen-bond constraint takes an important role in understanding the novel properties of elasticity of supercoiled DNA polymer.Comment: 21 pages, 6 PS figures. To appear at Biophys.

Mathematical Simulations in Topology and Their Role in Mathematics Education

This thesis presents and discusses several software projects related to the learning of mathematics in general and topological concepts in particular, collecting the results from several publications in this field. It approaches mathematics education by construction of mathematical learning environments, which can be used for the learning of mathematics, as well as by contributing insights gained during the development and use of these learning environments. It should be noted that the presented software environments were not built for the use in schools or other settings, but to provide proofs of concepts and to act as a basis for research into mathematics and its education and communication. The first developed and analyzed environment is Ariadne, a software for the interactive visualization of dots, paths, and homotopies of paths. Ariadne is used as an example of a “mathematical simulation”, capable of supporting argumentation in a way that may be characterized as proving. The software was extended from two to three dimensions, making possible the investigation of two-dimensional manifolds, such as the torus or the sphere, using virtual reality. Another extension, KnotPortal, enables the exploration of three-dimensional manifolds represented as branched covers of knots, after an idea by Bill Thurston to portray these branched covers of knots as knotted portals between worlds. This software was the motivation for and was used in an investigation into embodied mathematics learning, as this virtual reality environment challenges users to determine the structure of the covering by moving their body. Also presented are some unpublished projects that were not completed during the doctorate. This includes work on concept images in topology as well as software for various purposes. One such software was intended for the construction of closed orientable surfaces, while another was focused on the interactive visualization of the uniformization theorem. The thesis concludes with a meta-discussion on the role of design in mathematics education research. While design plays an important role in mathematics education, designing seems to not to be recognized as research in itself, but only as part of theory building or, in most cases, an empirical study. The presented argumentation challenges this view and points out the dangers and obstacles involved

A computer-generated supercoiled model of the pUC19 plasmid

DNA models have become a powerful tool in the simulation of radiation-induced molecular damage. Here, a computer code was developed which calculates the coordinates of individual atoms in supercoiled plasmid DNA. In this prototype study, the known base-pair sequence of the pUC19 plasmid has been utilized. The model was built in a three-step process. Firstly, a Monte Carlo simulation was performed to shape a segment chain skeleton. Checks on elastic energy, distance and unknotting were applied. The temperature was considered in two different ways: (1) it was kept constant at 293 K and (2) it was gradually reduced from 350 K to less than 10 K. Secondly, a special smoothing procedure was introduced here to remove the edges from the segment chain without changing the total curve length while avoiding the production of overshooting arcs. Finally, the base pair sequence was placed along the smoothed segment chain and the positions of all the atoms were calculated. As a first result, a few examples of the supercoiled plasmid models will be presented, demonstrating the strong influence of appropriate control of the system temperature

Evaluation of the usefulness of various simulation technology options for TERPS enhancement

Current approved terminal instrument procedures (TERPS) do not permit the full exploitation of the helicopter's unique flying characteristics. Enhanced TERPS need to be developed for a host of non-standard landing sites and navigation aids. Precision navigation systems such as microwave landing systems (MLS) and the Global Positioning System (GPS) open the possibility of curved paths, steep glide slopes, and decelerating helicopter approaches. This study evaluated the feasibility, benefits, and liabilities of using helicopter cockpit simulators in place of flight testing to develop enhanced TERPS criteria for non-standard flight profiles and navigation equipment. Near-term (2 to 5 year) requirements for conducting simulator studies to verify that they produce suitable data comparable to that obtained from previous flight tests are discussed. The long-term (5 to 10 year) research and development requirements to provide necessary modeling for continued simulator-based testing to develop enhanced TERPS criteria are also outlined

NEPTUNE: Non-Entangling Planning for Multiple Tethered Unmanned Vehicles

Despite recent progress on trajectory planning of multiple robots and path planning of a single tethered robot, planning of multiple tethered robots to reach their individual targets without entanglements remains a challenging problem. In this paper, we present a complete approach to address this problem. Firstly, we propose a multi-robot tether-aware representation of homotopy, using which we can efficiently evaluate the feasibility and safety of a potential path in terms of (1) the cable length required to reach a target following the path, and (2) the risk of entanglements with the cables of other robots. Then, the proposed representation is applied in a decentralized and online planning framework that includes a graph-based kinodynamic trajectory finder and an optimization-based trajectory refinement, to generate entanglement-free, collision-free and dynamically feasible trajectories. The efficiency of the proposed homotopy representation is compared against existing single and multiple tethered robot planning approaches. Simulations with up to 8 UAVs show the effectiveness of the approach in entanglement prevention and its real-time capabilities. Flight experiments using 3 tethered UAVs verify the practicality of the presented approach.Comment: Accepted for publication in IEEE Transaction on Robotic

Computational Geometric and Algebraic Topology

Computational topology is a young, emerging field of mathematics that seeks out practical algorithmic methods for solving complex and fundamental problems in geometry and topology. It draws on a wide variety of techniques from across pure mathematics (including topology, differential geometry, combinatorics, algebra, and discrete geometry), as well as applied mathematics and theoretical computer science. In turn, solutions to these problems have a wide-ranging impact: already they have enabled significant progress in the core area of geometric topology, introduced new methods in applied mathematics, and yielded new insights into the role that topology has to play in fundamental problems surrounding computational complexity. At least three significant branches have emerged in computational topology: algorithmic 3-manifold and knot theory, persistent homology and surfaces and graph embeddings. These branches have emerged largely independently. However, it is clear that they have much to offer each other. The goal of this workshop was to be the first significant step to bring these three areas together, to share ideas in depth, and to pool our expertise in approaching some of the major open problems in the field