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1. Knot polynomials of open and closed curves

   https://doi.org/10.1098/rspa.2020.0124  

   Panagiotou, Eleni ; Kauffman, Louis H. ( August 2020 , Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences)

   null (Ed.)

   In this manuscript, we introduce a method to measure entanglement of curves in 3-space that extends the notion of knot and link polynomials to open curves. We define the bracket polynomial of curves in 3-space and show that it has real coefficients and is a continuous function of the curve coordinates. This is used to define the Jones polynomial in a way that it is applicable to both open and closed curves in 3-space. For open curves, the Jones polynomial has real coefficients and it is a continuous function of the curve coordinates and as the endpoints of the curve tend to coincide, the Jones polynomial of the open curve tends to that of the resulting knot. For closed curves, it is a topological invariant, as the classical Jones polynomial. We show how these measures attain a simpler expression for polygonal curves and provide a finite form for their computation in the case of polygonal curves of 3 and 4 edges. 

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2. The Jones polynomial of collections of open curves in 3-space

   https://doi.org/10.1098/rspa.2022.0302  

   Barkataki, Kasturi ; Panagiotou, Eleni ( November 2022 , Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences)

   Measuring the entanglement complexity of collections of open curves in 3-space has been an intractable, yet pressing mathematical problem, relevant to a plethora of physical systems, such as in polymers and biopolymers. In this manuscript, we give a novel definition of the Jones polynomial that generalizes the classic Jones polynomial to collections of open curves in 3-space. More precisely, first we provide a novel definition of the Jones polynomial of linkoids (open link diagrams) and show that this is a well-defined single variable polynomial that is a topological invariant, which, for link-type linkoids, coincides with that of the corresponding link. Using the framework introduced in (Panagiotou E, Kauffman L. 2020 Proc. R. Soc. A 476 , 20200124. (( doi:10.1098/rspa.2020.0124 )), this enables us to define the Jones polynomial of collections of open and closed curves in 3-space. For collections of open curves in 3-space, the Jones polynomial has real coefficients and it is a continuous function of the curves’ coordinates. As the endpoints of the curves tend to coincide, the Jones polynomial tends to that of the resultant link. We demonstrate with numerical examples that the novel Jones polynomial enables us to characterize the topological/geometrical complexity of collections of open curves in 3-space for the first time. 

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3. The second Vassiliev measure of uniform random walks and polygons in confined space

   https://doi.org/10.1088/1751-8121/ac4abf  

   Smith, Philip ; Panagiotou, Eleni ( February 2022 , Journal of Physics A: Mathematical and Theoretical)

   Abstract Biopolymers, like chromatin, are often confined in small volumes. Confinement has a great effect on polymer conformations, including polymer entanglement. Polymer chains and other filamentous structures can be represented by polygonal curves in three-space. In this manuscript, we examine the topological complexity of polygonal chains in three-space and in confinement as a function of their length. We model polygonal chains by equilateral random walks in three-space and by uniform random walks (URWs) in confinement. For the topological characterization, we use the second Vassiliev measure. This is an integer topological invariant for polygons and a continuous functions over the real numbers, as a function of the chain coordinates for open polygonal chains. For URWs in confined space, we prove that the average value of the Vassiliev measure in the space of configurations increases as O ( n 2 ) with the length of the walks or polygons. We verify this result numerically and our numerical results also show that the mean value of the second Vassiliev measure of equilateral random walks in three-space increases as O ( n ). These results reveal the rate at which knotting of open curves and not simply entanglement are affected by confinement. 

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4. Fréchet Distance for Uncertain Curves

   https://doi.org/10.1145/3597640  

   Buchin, Kevin ; Fan, Chenglin ; Löffler, Maarten ; Popov, Aleksandr ; Raichel, Benjamin ; Roeloffzen, Marcel ( July 2023 , ACM Transactions on Algorithms)

   In this article, we study a wide range of variants for computing the (discrete and continuous) Fréchet distance between uncertain curves. An uncertain curve is a sequence of uncertainty regions, where each region is a disk, a line segment, or a set of points. A realisation of a curve is a polyline connecting one point from each region. Given an uncertain curve and a second (certain or uncertain) curve, we seek to compute the lower and upper bound Fréchet distance, which are the minimum and maximum Fréchet distance for any realisations of the curves. We prove that both problems are NP-hard for the Fréchet distance in several uncertainty models, and that the upper bound problem remains hard for the discrete Fréchet distance. In contrast, the lower bound (discrete [ 5 ] and continuous) Fréchet distance can be computed in polynomial time in some models. Furthermore, we show that computing the expected (discrete and continuous) Fréchet distance is #P-hard in some models. On the positive side, we present an FPTAS in constant dimension for the lower bound problem when Δ/δ is polynomially bounded, where δ is the Fréchet distance and Δ bounds the diameter of the regions. We also show a near-linear-time 3-approximation for the decision problem on roughly δ-separated convex regions. Finally, we study the setting with Sakoe–Chiba time bands, where we restrict the alignment between the curves, and give polynomial-time algorithms for the upper bound and expected discrete and continuous Fréchet distance for uncertainty modelled as point sets. 

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5. Hölder Parameterization of Iterated Function Systems and a Self-Aflne Phenomenon

   https://doi.org/10.1515/agms-2020-0125  

   Badger, Matthew ; Vellis, Vyron ( January 2021 , Analysis and Geometry in Metric Spaces)

   null (Ed.)

   Abstract We investigate the Hölder geometry of curves generated by iterated function systems (IFS) in a complete metric space. A theorem of Hata from 1985 asserts that every connected attractor of an IFS is locally connected and path-connected. We give a quantitative strengthening of Hata’s theorem. First we prove that every connected attractor of an IFS is (1/ s )-Hölder path-connected, where s is the similarity dimension of the IFS. Then we show that every connected attractor of an IFS is parameterized by a (1/ α)-Hölder curve for all α > s . At the endpoint, α = s , a theorem of Remes from 1998 already established that connected self-similar sets in Euclidean space that satisfy the open set condition are parameterized by (1/ s )-Hölder curves. In a secondary result, we show how to promote Remes’ theorem to self-similar sets in complete metric spaces, but in this setting require the attractor to have positive s -dimensional Hausdorff measure in lieu of the open set condition. To close the paper, we determine sharp Hölder exponents of parameterizations in the class of connected self-affine Bedford-McMullen carpets and build parameterizations of self-affine sponges. An interesting phenomenon emerges in the self-affine setting. While the optimal parameter s for a self-similar curve in ℝ n is always at most the ambient dimension n , the optimal parameter s for a self-affine curve in ℝ n may be strictly greater than n . 

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