arXiv subjects

Jason Cantarella

Publications and source records attributed to Jason Cantarella.

At least 19 recordsLinked to original sources

arXiv2026

Hard unknots are often easy from a different perspective

Recent attempts to train AI models to recognize knots have produced millions of ``hard'' unknot diagrams resistant to simplification by Reidemeister moves, pass moves, or random walks on the Reidemeister graph. Most are easy for the methods based on triangulations of the knot complement found in Regina and SnapPy, but more difficult for simplifiers based on diagrammatic moves. We present ReAPR (Re-embedding And Pass Rerouting), a semi-diagrammatic simplifier which alternates pass-move reduction on a knot diagram with a geometric re-embedding step. The re-embedding minimizes the total variation of a height function on the diagram subject to crossing constraints. We show that for an n-crossing diagram, the minimum total variation is 2(n-k), where k is the least number of crossings one must virtualize to make the diagram virtually alternating; this is a combinatorial invariant of the diagram. Reprojecting the resulting embedding from a new viewpoint reveals previously hidden simplifications. ReAPR successfully simplifies every published hard-unknot example we are aware of, as well as several new collections (~2.6 million examples in total) in under 30 seconds of total CPU time, making it as effective as the best non-diagrammatic unknot recognition method (SnapPy) and about 60x faster. ReAPR is just as effective at simplifying diagrams of random knots, where it is regularly used to simplify diagrams with tens of millions of crossings.

math.GT↗

arXiv2026

Random knotting in very long off-lattice self-avoiding polygons

We present experimental results on knotting in off-lattice self-avoiding polygons in the bead-chain model. Using Clisby's tree data structure and the scale-free pivot algorithm, for each $k$ between $10$ and $27$ we generated $2^{43-k}$ polygons of size $n=2^k$. Using a new knot diagram simplification and invariant-free knot classification code, we were able to determine the precise knot type of each polygon. The results show that the number of prime summands of knot type $K$ in a random $n$-gon is very well described by a Poisson distribution. We estimate the characteristic length of knotting as $656500 \pm 2500$. We use the count of summands for large $n$ to measure knotting rates and amplitude ratios of knot probabilities more accurately than previous experiments. Our calculations agree quite well with previous on-lattice computations, and support both knot localization and the knot entropy conjecture.

cond-mat.stat-mech↗

arXiv2025

Factoring the Laplacian to understand topological polymers

A ring polymer is a random walk whose steps obey a single linear condition; their sum vanishes. Factoring the graph Laplacian into the product of the incidence matrix and its transpose allows us to show that for a more complicated network, the steps must lie in a linear subspace determined by the graph topology. This provides a useful new perspective on the James--Guth theory of phantom elastic networks. In particular, we formulate phantom networks which are free from the constraints of fixed crosslinks. For a given network the solution of the loop constraints makes the partition function finite-valued in the path integral formulation without applying any external forces or fixing any monomer positions. The resulting probability distribution on edge displacements is rotationally invariant, which is practically quite useful for generating unbiased random samples of edge displacements and monomer positions. Furthermore, one can exactly calculate many physical quantities such as correlation functions with respect to this distribution. Finally, this reformulation lends itself well to the case of non-Gaussian distributions. We illustrate this by computing the expected radius of gyration of a ring polymer in a wide variety of models.

cond-mat.stat-mech↗

arXiv2025

New Upper Bounds for Stick Numbers

We use a version of simulated annealing with knot-type preserving moves to find polygonal representatives of various knot types with low stick number. These give better bounds on stick numbers of prime knots through 10 crossings, and for the first time give a comprehensive table of stick number bounds on all knots through 13 crossings. These are equal to existing lower bounds (and hence determine the stick number exactly) for 19 knot types whose exact stick number was not known previously.

math.GT↗

arXiv2025

An exact formula for the contraction factor of a subdivided Gaussian topological polymer

We consider the radius of gyration of a Gaussian topological polymer $G$ formed by subdividing a graph $G'$ of arbitrary topology (for instance, branched or multicyclic). We give a new exact formula for the expected radius of gyration and contraction factor of $G$ in terms of the number of subdivisions of each edge of $G'$ and a new weighted Kirchhoff index for $G'$. The formula explains and extends previous results for the contraction factor and Kirchhoff index of subdivided graphs.

cond-mat.stat-mech↗

arXiv2024

On the average squared radius of gyration of a family of embeddings of subdivision graphs

Suppose we have an embedding of a graph $\mathbf{G}$ created by subdividing the edges of a simpler graph $\mathbf{G'}$. The edges of $\mathbf{G}$ can be divided into subsets which join pairs of ``junction'' vertices in $\mathbf{G'}$. The displacement vectors of the edges in each subset sum to the displacement between junctions. We can construct a family of embeddings of $\mathbf{G}$ with the same junction positions by rearranging the displacements in each group. In this paper, we show that the average (squared) radius of gyration of these embeddings is given by a simple formula involving a weighted (squared) radius of gyration of the positions of the junctions and the sum of the squares of the lengths of the edges of $\mathbf{G}$ and $\mathbf{G'}$. This ensemble of graph embeddings arises naturally in polymer science.

math.CO↗

arXiv2024

A faster direct sampling algorithm for equilateral closed polygons and the probability of knotting

We present a faster direct sampling algorithm for random equilateral closed polygons in three-dimensional space. This method improves on the moment polytope sampling algorithm of Cantarella, Duplantier, Shonkwiler, and Uehara (2016) and has (expected) time per sample quadratic in the number of edges in the polygon. We use our new sampling method and a new code for computing invariants based on the Alexander polynomial to investigate the probability of finding unknots among equilateral closed polygons.

cond-mat.stat-mech↗

arXiv2023

CoBarS: Fast reweighted sampling for polygon spaces in any dimension

We present the first algorithm for sampling random configurations of closed $n$-gons with any fixed edgelengths $r_1, \dots, r_n$ in any dimension $d$ which is proved to sample correctly from standard probability measures on these spaces. We generate open $n$-gons as weighted sets of edge vectors on the unit sphere and close them by taking a Möbius transformation of the sphere which moves the center of mass of the edges to the origin. Using previous results of the authors, such a Möbius transformation can be found in $O(n)$ time. The resulting closed polygons are distributed according to a pushforward measure. The main contribution of the present paper is the explicit calculation of reweighting factors which transform this pushforward measure to any one of a family of standard measures on closed polygon space, including the symplectic volume for polygons in $\mathbb{R}^3$. For fixed dimension, these reweighting factors may be computed in $O(n)$ time. Experimental results show that our algorithm is efficient and accurate in practice, and an open-source reference implementation is provided.

math.DG↗

arXiv2022

Radius of Gyration, Contraction Factors, and Subdivisions of Topological Polymers

We consider the topologically constrained random walk model for topological polymers. In this model, the polymer forms an arbitrary graph whose edges are selected from an appropriate multivariate Gaussian which takes into account the constraints imposed by the graph type. We recover the result that the expected radius of gyration can be given exactly in terms of the Kirchhoff index of the graph. We then consider the expected radius of gyration of a topological polymer whose edges are subdivided into $n$ pieces. We prove that the contraction factor of a subdivided polymer approaches a limit as the number of subdivisions increases, and compute the limit exactly in terms of the degree-Kirchhoff index of the original graph. This limit corresponds to the thermodynamic limit in statistical mechanics and is fundamental in the physics of topological polymers. Furthermore, these asymptotic contraction factors are shown to fit well with molecular dynamics simulations.

cond-mat.stat-mech↗

arXiv2022

Families of similar simplices inscribed in most smoothly embedded spheres

Let $Δ$ denote a non-degenerate $k$-simplex in $\mathbb{R}^k$. The set $\text{Sim}(Δ)$ of simplices in $\mathbb{R}^k$ similar to $Δ$ is diffeomorphic to $O(k)\times [0,\infty)\times \mathbb{R}^k$, where the factor in $O(k)$ is a matrix called the {\em pose}. Among $(k-1)$-spheres smoothly embedded in $\mathbb{R}^k$ and isotopic to the identity, there is a dense family of spheres, for which the subset of $\text{Sim}(Δ)$ of simplices inscribed in each embedded sphere contains a similar simplex of every pose $U\in O(k)$. Further, the intersection of $\text{Sim}(Δ)$ with the configuration space of $k+1$ distinct points on an embedded sphere is a manifold whose top homology class maps to the top class in $O(k)$ via the pose map. This gives a high dimensional generalization of classical results on inscribing families of triangles in plane curves. We use techniques established in our previous paper on the square-peg problem where we viewed inscribed simplices in spheres as transverse intersections of submanifolds of compactified configuration spaces.

math.GT↗

arXiv2022

Configuration Spaces, Multijet Transversality, and the Square-Peg Problem

We prove a transversality "lifting property" for compactified configuration spaces as an application of the multijet transversality theorem: given a submanifold of configurations of points on an embedding of a compact manifold $M$ in Euclidean space, we can find a dense set of smooth embeddings of $M$ for which the corresponding configuration space of points is transverse to any submanifold of the configuration space of points in Euclidean space, as long as the two submanifolds of compactified configuration space are boundary-disjoint. We use this setup to provide an attractive proof of the square-peg problem: there is a dense family of smoothly embedded circles in the plane where each simple closed curve has an odd number of inscribed squares, and there is a dense family of smoothly embedded circles in $\mathbb{R}^n$ where each simple closed curve has an odd number of inscribed square-like quadrilaterals.

math.GT↗

arXiv2022

Random graph embeddings with general edge potentials

In this paper, we study random embeddings of polymer networks distributed according to any potential energy which can be expressed in terms of distances between pairs of monomers. This includes freely jointed chains, steric effects, Lennard-Jones potentials, bending energies, and other physically realistic models. A configuration of $n$ monomers in $\mathbb{R}^d$ can be written as a collection of $d$ coordinate vectors, each in $\mathbb{R}^n$. Our first main result is that entries from different coordinate vectors are uncorrelated, even when they are different coordinates of the same monomer. We predict that this property holds in realistic simulations and in actual polymer configurations (in the absence of an external field). Our second main contribution is a theorem explaining when and how a probability distribution on embeddings of a complicated graph may be pushed forward to a distribution on embeddings of a simpler graph to aid in computations. This construction is based on the idea of chain maps in homology theory. We use it to give a new formula for edge covariances in phantom network theory and to compute some expectations for a freely-jointed network.

cond-mat.stat-mech↗

arXiv2021

Transversality for Configuration Spaces and the "Square-Peg" Theorem

We prove a transversality "lifting property" for compactified configuration spaces as an application of the multijet transversality theorem: the submanifold of configurations of points on an arbitrary submanifold of Euclidean space may be made transverse to any submanifold of the configuration space of points in Euclidean space by an arbitrarily $C^1$-small variation of the initial submanifold, as long as the two submanifolds of compactified configuration space are boundary-disjoint. We use this setup to provide attractive proofs of the existence of a number of "special inscribed configurations" inside families of spheres embedded in $\mathbb{R}^n$ using differential topology. For instance, there is a $C^1$-dense family of smooth embedded circles in the plane where each simple closed curve has an odd number of inscribed squares, and there is a $C^1$-dense family of smooth embedded $(n-1)$-spheres in $\mathbb{R}^n$ where each sphere has a family of inscribed regular $n$-simplices with the homology of $O(n)$.

math.GT↗

arXiv2021

Square-like quadrilaterals inscribed in embedded space curves

The square-peg problem asks if every Jordan curve in the plane has four points which are the vertices of a square. The problem is open for continuous Jordan curves, but it has been resolved for various regularity classes of curves between continuous and $C^1$-smooth Jordan curves. Here, in a generalization of the square-peg problem, we consider embedded curves in space, and ask if they have inscribed quadrilaterals with equal sides and equal diagonals. We call these quadrilaterals "square-like". We give a regularity class (finite total curvature without cusps) in which we can prove that every embedded curve has an inscribed square-like quadrilateral. The key idea is to use local data to show that short enough arcs have small curvature, thus ruling out small squares. This allows us to successfully use a limiting argument on approximating curves.

math.DG↗

arXiv2020

Performance of the Uniform Closure Method for open knotting as a Bayes-type classifier

The discovery of knotting in proteins and other macromolecular chains has motivated researchers to more carefully consider how to identify and classify knots in open arcs. Most definitions classify knotting in open arcs by constructing an ensemble of closures and measuring the probability of different knot types among these closures. In this paper, we think of assigning knot types to open curves as a classification problem and compare the performance of the Bayes MAP classifier to the standard Uniform Closure Method. Surprisingly, we find that both methods are essentially equivalent as classifiers, having comparable accuracy and positive predictive value across a wide range of input arc lengths and knot types.

math.GT↗

arXiv2020

Computing the conformal barycenter

The conformal barycenter of a point cloud on the sphere at infinity of the Poincaré ball model of hyperbolic space is a hyperbolic analogue of the geometric median of a point cloud in Euclidean space. It was defined by Douady and Earle as part of a construction of a conformally natural way to extend homeomorphisms of the circle to homeomorphisms of the disk, and it plays a central role in Millson and Kapovich's model of the configuration space of cyclic linkages with fixed edgelengths. In this paper we consider the problem of computing the conformal barycenter. Abikoff and Ye have given an iterative algorithm for measures on $\mathbb{S}^1$ which is guaranteed to converge. We analyze Riemannian versions of Newton's method computed in the intrinsic geometry of the Poincare ball model. We give Newton-Kantorovich (NK) conditions under which we show that Newton's method with fixed step size is guaranteed to converge quadratically to the conformal barycenter for measures on any $\mathbb{S}^d$ (including infinite-dimensional spheres). For measures given by $n$ atoms on a finite dimensional sphere which obey the NK conditions, we give an explicit linear bound on the computation time required to approximate the conformal barycenter to fixed error. We prove that our NK conditions hold for all but exponentially few $n$ atom measures. For all measures with a unique conformal barycenter we show that a regularized Newton's method with line search will always converge (eventually superlinearly) to the conformal barycenter. Though we do not have hard time bounds for this algorithm, experiments show that it is extremely efficient in practice and in particular much faster than the Abikoff-Ye iteration.

math.DG↗

arXiv2018

Open and closed random walks with fixed edgelengths in $\mathbb{R}^d$

In this paper, we consider fixed edgelength $n$-step random walks in $\mathbb{R}^d$. We give an explicit construction for the closest closed equilateral random walk to almost any open equilateral random walk based on the geometric median, providing a natural map from open polygons to closed polygons of the same edgelength. Using this, we first prove that a natural reconfiguration distance to closure converges in distribution to a Nakagami$(\frac{d}{2},\frac{d}{d-1})$ random variable as $n \rightarrow \infty$. We then strengthen this to an explicit probabilistic bound on the distance to closure for a random $n$-gon in any dimension with any collection of fixed edgelengths $w_i$. Numerical evidence supports the conjecture that our closure map pushes forward the natural probability measure on open polygons to something very close to the natural probability measure on closed polygons; if this is so, we can draw some conclusions about the frequency of local knots in closed polygons of fixed edgelength.

cond-mat.stat-mech↗

arXiv2017

Knot Fertility and Lineage

In this paper, we introduce a new type of relation between knots called the descendant relation. One knot $H$ is a descendant of another knot $K$ if $H$ can be obtained from a minimal crossing diagram of $K$ by some number of crossing changes. We explore properties of the descendant relation and study how certain knots are related, paying particular attention to those knots, called fertile knots, that have a large number of descendants. Furthermore, we provide computational data related to various notions of knot fertility and propose several open questions for future exploration.

math.GT↗