Thesis advisor: John A. Baldwin / We classify genus-two L-space knots in S3 and the Poincare homology sphere.This leads to the first and to-date only detection results in knot Floer homology for knots of genus greater than one. Our proofs interweave Floer-homological properties of L-space knots, the geometry of pseudo-Anosov maps, and the theory of train tracks and folding automata for braids. The crux of our argument is a complete classification of fixed-point-free pseudo-Anosov maps in all but one stratum on the genus-two surface with one boundary component. To facilitate our classification, we exhibit a small family of train tracks carrying all pseudo-Anosov maps in most strata on the marked disk. As a consequence of our proof technique, we almost completely classify genus-two, hyperbolic, fibered knots with knot Floer homology of rank 1 in their next-to-top grading in any 3-manifold. Several corollaries follow, regarding the Floer homology of cyclic branched covers, SU(2)-abelian Dehn surgeries, Khovanov and annular Khovanov homology, and instanton Floer homology. / Thesis (PhD) — Boston College, 2024. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Mathematics.

This dissertation studies quantum invariants of knots and links, particularly the colored Jones polynomials, and their relationships with classical invariants like the hyperbolic volume and the A-polynomial. We consider the volume conjecture that relates the Kashaev invariant, a specialization of the colored Jones polynomial at a specific root of unity, and the hyperbolic volume of a link; and the AJ conjecture that relates the colored Jones polynomial and the A-polynomial of a knot. We establish the AJ conjecture for some big classes of two-bridge knots and pretzel knots, and confirm the volume conjecture for some cables of knots.

Many biomolecular processes involve mechanical force-induced reactions in the cell, such as translocation, and mechanical stretching of biopolymers. Recent advances in single molecule manipulation techniques make it possible to apply mechanical force to individual biomolecules and study their dynamics. To gain molecular level understanding of these processes and to interpret the single-molecule experiments, we used Langevin dynamics simulations of coarse-grained biopolymer models. Our result show that the mechanism of translocation of proteins through pores depends on the pore diameter, on the magnitude of the pulling force and on whether the force is applied at the N- or the C-terminus of the chain. In addition, the translocation kinetics of peptides varies with their stability. The mechanism of protein translocation is found to be different from that of a structureless polypeptide of the same length. We further showed that unfolding mechanism of translocation process is different from when the same protein is stretched between its C- and N-termini. We also studied the mechanical and chemical/thermal denaturation of proteins. We observed that the free energy profile along the mechanical reaction coordinate and the chemical reaction coordinate are different. In our protein model, the mechanical and chemical/thermal denaturation cannot be simply explained in terms of a simple onedimensional free energy landscape. We further analyzed the spontaneous folding and refolding under a constant force and found that refolding generally occurs via different mechanisms. Similarly, we investigated the protein unfolding/refolding under the applied force that varies with a constant loading rate. This study shows that unfolding/refolding pathways are generally similar for low loading/unloading rates while they become different for high loading/unloading rates. Finally, we studied the dynamics of molecular friction knots formed by a pair of polymer strands. We examined different knot types, and different polymer sequences. Depending on the knot type and the nature of the polymer, we observed two different behaviors when the force F is exerted to separate the polymer strands. The knot between polymer strands can be strong (the time [tau] the knot stays tied increases with the force F applied to separate the strands) or weak ([tau]decreases with increasing F).

Le but de cette thèse est de fournir une caractérisation topologique de tresses virtuelles. Les tresses virtuelles sont des classes d’équivalence de diagrammes de type tresses tracés sur le plan. La relation d’équivalence est générée par l’isotopie, les mouvements de Reidemeister et les mouvements de Reidemeister virtuels. L’ensemble des tresses virtuelles est munie d’une opération de groupe. On parlera alors du groupe de tresses virtuelles. Dans le Chapitre 1, nous introduisons les notions de base de la théorie de noeuds virtuels, nous évoquons certains propriétés du groupe tresses virtuelles, et des liens qu’il a avec le groupe de tresses classiques. Dans le Chapitre 2, nous introduisons la notion de diagramme de Gauss tressé (ou diagramme de Gauss horizontal), et on démontre qu’il s’agit là d’une bonne réinterprétation combinatoire pour les tresses virtuelles. On généralise en particulier certains résultats connus en théorie de noeuds virtuels. Un application est de retrouver la présentation classique du groupe de tresses virtuelles pures à l’aide des diagrammes de Gauss tressés. Dans le Chapitre 3, on introduit les tresses abstraites et on montre qu’elles sont en correspondance bijective avec les tresses virtuelles. Les tresses abstraites sont des classes d’équivalence des diagrammes de type tresses tracés sur une surface orientable avec deux composantes de bord. La relation d’équivalence est générée par l’isotopie, la compatibilité, la stabilité et les mouvements de Reidemeister. La compatibilité est la relation d’équivalence générée par les difféomorphismes préservant l’orientation. La stabilité est la relation d’équivalence générée par l’addition ou la suppression d’anses à la surface, dans le complémentaire du diagramme. Dans le Chapitre 4, on démontre que tout tresse abstraite admets une unique représentant de genre minimal, à compatibilité et mouvements de Reidemeister prés. En particulier, les tresses classiques se plongent dans les tresses abstraites. / The purpose of this thesis is to give a topological characterization of virtual braids. Virtual braids are equivalence classes of planar braid-like diagrams identified up to isotopy, Reidemeister and virtual Reidemeister moves. The set of virtual braids admits a group structure and is called the virtual braid group. In Chapter 1 we present a general introduction to the theory of virtual knots, and we discuss some properties of virtual braids and their relations with classical braids. In Chapter 2 we introduce braid-Gauss dia- grams, and we prove that they are a good combinatorial reinterpretation of virtual braids. In particular this generalizes some results known in virtual knot theory. As an application, we use braid-Gauss diagrams to recover a well known presentation of the pure virtual braid group. In Chapter 3 we introduce abstract braids and we prove that they are in a bijective cor- respondence with virtual braids. Abstract braids are equivalence classes of braid-like diagrams on an orientable surface with two boundary components. The equivalence relation is generated by isotopy, compatibility, stability and Reidemeister moves. Compatibility is the equivalence relation generated by orientation preserving diffeomorphisms. Stability is the equivalence relation generated by adding handles to or deleting handles from the surface in the complement of the braid-like diagram. In Chapter 4 we prove that for any abstract braid, there is a unique representative of minimal genus, up to compatibility and Reidemeister equivalence. In particular this implies that classical braids embed in abstract braids.

<p>This thesis investigates aspects of field theories and soliton solutions with nontrivial topology. In particular we explore the following effective models: a limited sector of the scalar Electroweak theory called extended Abelian Higgs model, and a classical mechanics model derived from the low energy SU(2) Yang-Mills theory.</p><p>The extended Abelian Higgs model applied on two-component plasma of charged particles is studied numerically. We find evidence that the model admits straight twisted line vortices. The result is described by an energy function that acquires a minimum value for a non-trivial twist. In addition to the twisted line vortices the result also suggests that stable torus shaped solitons are solutions of the theory. </p><p>Furthermore we construct a classical mechanics model exhibiting some of the key properties of the low-energy Yang-Mills theory. The dynamics of the model is studied numerically. We find that its classical equations of motion support stable periodic orbits. In a three dimensional projection these trajectories are self-linked in a topologically non-trivial manner suggesting the existence of knotted configurations in low energy SU(2) Yang-Mills theory. </p><p>We calculate the one-loop effective action for the Abelian Higgs model with extended Higgs sector. The resulting first order quantum corrected model shows close resemblance to a modified model where texture stabilizing term has been added to the system. In the limit where the gauge field can be entirely expressed by the scalar fields, the both models become identical suggesting that the theories are closely connected. This implies that quantum corrections have stabilising effect on the soliton solutions. </p><p>These studies have contributed to a better understanding of the dynamics of non-linear low energy systems, and brought us a step closer to exploring full scale physically realistic models.</p>

This thesis investigates aspects of field theories and soliton solutions with nontrivial topology. In particular we explore the following effective models: a limited sector of the scalar Electroweak theory called extended Abelian Higgs model, and a classical mechanics model derived from the low energy SU(2) Yang-Mills theory. The extended Abelian Higgs model applied on two-component plasma of charged particles is studied numerically. We find evidence that the model admits straight twisted line vortices. The result is described by an energy function that acquires a minimum value for a non-trivial twist. In addition to the twisted line vortices the result also suggests that stable torus shaped solitons are solutions of the theory. Furthermore we construct a classical mechanics model exhibiting some of the key properties of the low-energy Yang-Mills theory. The dynamics of the model is studied numerically. We find that its classical equations of motion support stable periodic orbits. In a three dimensional projection these trajectories are self-linked in a topologically non-trivial manner suggesting the existence of knotted configurations in low energy SU(2) Yang-Mills theory. We calculate the one-loop effective action for the Abelian Higgs model with extended Higgs sector. The resulting first order quantum corrected model shows close resemblance to a modified model where texture stabilizing term has been added to the system. In the limit where the gauge field can be entirely expressed by the scalar fields, the both models become identical suggesting that the theories are closely connected. This implies that quantum corrections have stabilising effect on the soliton solutions. These studies have contributed to a better understanding of the dynamics of non-linear low energy systems, and brought us a step closer to exploring full scale physically realistic models.

Η τοπολογική ταξινόμηση και μελέτη διανυσματικών πεδίων αποτελεί το κύριο θέμα αυτής της διατριβής. Στο Κεφάλαιο 1 δίνονται οι απαραίτητοι ορισμοί, καθώς και τα αποτελέσματα επί της ταξινόμησης διανυσματικών πεδίων σε μονοδιάστατες και δισδιάτατες πολλαπλότητες. Στο Κεφάλαιο 2 τεχνικές της Θεωρίας Κόμβων χρησιμοποιούνται προκειμένου να μελετηθεί η τοπολογική δομή ορισμένων παράξενων ελκυστών που εμφανίζονται στη διεθνή βιβλιογραφία. Στο Κεφάλαιο 3 αναπτύσσεται μία μέθοδος η οποία επιτρέπει την ολική τοπολογική ταξινόμηση διανυσματικών πεδίων σε ευκλείδειους χώρους οποιασδήποτε διάστασης. Η μέθοδος αυτή έπειτα εφαρμόζεται στην ταξινόμηση διανυσματικών πεδίων του R^2 και του R^3. Στο Κεφάλαιο 4 μελετάται ένα διανυσματικό πεδίο του R^3 αμετάβλητο από την D_2 ομάδα. Δίνεται η ολική του μελέτη, για διάφορες τιμές των παραμέτρων, και το μερικό του διάγραμμα διακλάδωσης. Αποδεικνύεται η ύπαρξη χάους και συνδέεται με τις συμμετρικές ιδιότητες του συστήματος, ενώ η μελέτη ολοκληρώνεται με τη συμπεριφορά του συστήματος στο άπειρο. / The topological classification and study of vector fields is the subject of this thesis. In Chapter 1 the necessary definitions are given, along with the known results on the classification of vector fields on 1-dimensional and 2-dimensional manifolds. In Chapter 2 methods of Knot Theory are used for the clarification of the topological study of some strange attractors found in the bibliography. In Chapter 3 a technique is developed, which can be used to classify globally vector fields defined on Euclidean spaces of any dimension. This technique is then used to classify some vector fields of R^2 and R^3. In the final Chapter 4 a vector field of R^3 is studied which is invariant under the D_2 symmetry group. We present its global phase portrait, for various parameter values, and its partial bifurcation diagram. The existence of chaos is proven and its connection to the symmetry properties of the attractor is discussed. We end its study presenting its behavior at infinity.

The 4-genus of a knot in S3 is an important measure of complexity, related to the unknotting number. A fundamental result used to study the 4-genus and related invariants of homology classes is the Thom conjecture, proved by Kronheimer-Mrowka, and its symplectic extension due to Ozsv´ath-Szab´o, which say that closed symplectic surfaces minimize genus. In this thesis, we prove a relative version of the symplectic capping theorem. More precisely, suppose (X, ω) is a symplectic 4-manifold with contact type bounday ∂X and Σ is a symplectic surface in X such that ∂Σ is a transverse knot in ∂X. We show that there is a closed symplectic 4-manifold Y with a closed symplectic submanifold S such that the pair (X, Σ) embeds symplectically into (Y, S). This gives a proof of the relative version of Symplectic Thom Conjecture. We use this to study 4-genus of fibered knots in S3 . We also prove a relative version of the sufficiency part of Giroux’s criterion for Stein fillability, namely, we show that a fibered knot whose mondoromy is a product of positive Dehn twists bounds a symplectic surface in a Stein filling. We use this to study 4-genus of fibered knots in S3 . Using this result, we give a criterion for quasipostive fibered knots to be strongly quasipositive. Symplectic convexity disc bundles is a useful tool in constructing symplectic fillings of contact manifolds. We show the symplectic convexity of the unit disc bundle in a Hermitian holomorphic line bundle over a Riemann surface.

The dissertation Alternative Ontology, subtitled Topological Imagination and Topological Materialism, focuses on the analysis of spatial phenomena and space in the intentions of the mathematical discipline of topology, which is interested in spaces from the point of view of set theory. My goal is to present topology as a tool not only for contemporary philosophy, but also for artistic creation. For the purpose of the dissertation, I formulate two concepts: Topological imagination and Topological materialism. Topological imagination is a tool and method for creating and thinking with the consciousness of space as a dynamic structure, which is not bound only by fixed laws of geometry. This method originated as the name of my long-term artistic practice, which is largely based on the study of space, topology, knot theory and the search for ways of their application in artistic and theoretical work. I propose Topological materialism as a concept that combines the thinking of networks and multi-dimensional spaces with the philosophical currents of the materialist tradition, especially the New Materialism. My basic thesis is that these cannot be perceived separately. Materialism cannot be thought without its spatial dimension, and topology without anchoring in the material world becomes a mere abstraction. The second part of the dissertation is devoted to the analysis of specific spaces: the space we inhabit, which I call phenomenological, infrastructure, logistics space, information space and the space of capital. In addition to individual analyzes, I also focus on their intersections, connections and joint operation.