The problem of finding the crossing number of an arbitrary knot or link is a hard problem in general. Only for very special classes of knots and links can we solve this problem. Often we can only hope to find a lower bound on the crossing number Cr(K) of a knot or a link K by computing the Jones polynomial of K, V(K). The crossing number Cr(K) is bounded from below by the difference between the greatest degree and the smallest degree of the polynomial V(K). However the computation of the Jones polynomial of an arbitrary knot or link is also difficult in general. The goal of this thesis is to find closed formulas for the smallest and largest exponents of the Jones polynomial for certain classes of knots and links. This allows us to find a lower bound on the crossing number for these knots and links very quickly. These formulas for the smallest and largest exponents of the Jones polynomial are constructed from special rational tangles expansions and using these formulas, we can extend these results to for [sic] special cases of Montesinos knots and links.

This dissertation studies the colored Jones polynomial of knots and links, colored by representations of simple Lie algebras, and the stability of its coefficients. Chapter 1 provides an explicit formula for the second plethysm of an arbitrary representation of sl3. This allows for an explicit formula for the colored Jones polynomial of the trefoil, and more generally, for T(2,n) torus knots. This formula for the sl3 colored Jones polynomial of T(2,n)$ torus knots makes it possible to verify the Degree Conjecture for those knots, to efficiently compute the sl3 Witten-Reshetikhin-Turaev invariants of the Poincare sphere, and to guess a Groebner basis for the recursion ideal of the sl3 colored Jones polynomial of the trefoil. Chapter 2 gives a formulation of a stability conjecture for the coefficients of the colored Jones polynomial of a knot, colored by irreducible representations in a fixed ray of a simple Lie algebra. The conjecture is verified for all torus knots and all simple Lie algebras of rank 2. Chapter 3 supplies an efficient method to compute those q-series that come from planar graphs (i.e., reduced Tait graphs of alternating links) and compute several terms of those series for all graphs with at most 8 edges. In addition, a graph-theory proof of a theorem of Dasbach-Lin which identifies the coefficient of q^k in those series for k=0,1,2 in terms of polynomials on the number of vertices, edges and triangles of the graph is given. Chapter 4 provides a study of the structure of the stable coefficients of the Jones polynomial of an alternating link.The first four stable coefficients are identified with polynomial invariants of a (reduced) Tait graph of the link projection. A free polynomial algebra of invariants of graphs whose elements give invariants of alternating links is introduced which strictly refines the first four stable coefficients. It is conjectured that all stable coefficients are elements of this algebra, and experimental evidence for the fifth and sixth stable coefficient is given. The results are illustrated in tables of all alternating links with at most 10 crossings and all irreducible planar graphs with at most 6 vertices.

We study the sl(3) web algebra via morphisms on foams. A pre-foam is a cobordism between two webs that contains singular arcs, which are sets of points whose neighborhoods are homeomorphic to the cross-product of the letter "Y'' and the unit interval. Pre-foams may have a distinguished point, and it can be moved around as long as it does not cross a singular arc. A foam is an isotopy class of pre-foams modulo a set of certain relations involving dots on the pre-foams. Composition in Foams is achieved by stacking pre-foams. We compute the cohomology ring of the sl(3) web algebra and apply a functor from the cohomology ring of the sl(3) web algebra to {\bf Foams}. Afterwards, we use this to study the $\mathfrak{sl}(3)$ web algebra via morphisms on foams.

The Jones polynomial is a special topological invariant in the field of Knot Theory. Created by Vaughn Jones, in the year 1984, it is used to study when links in space are topologically different and when they are topologically equivalent. This thesis discusses the Jones polynomial in depth as well as determines a general form for the closure of any braid in the braid group B2 where the closure is a knot. This derivation is facilitated by the help of the Temperley-Lieb algebra as well as with tools from the field of Abstract Algebra. In general, the Artin braid group Bn is the set of braids on n strands along with the binary operation of concatenation. This thesis also shows results of the relationship between the closure of a product of braids in B2 and the connected sum of the closure of braids in B2. Results on the topological invariant of tricolorability of closed braids in B2 and (2,n) torus links along with their obverses are presented as well.

My research area is applications of topology to biology, especially DNA topology. DNA topology studies the shape and path of DNA in three dimensional space. My thesis relates to the study of DNA topology in a protein-DNA complex by solving tangle equations and calculating distances between DNA knots.

This thesis has four chapters. After a brief introduction in Chapter 1, the $AJ$-conjecture is introduced in Chapter 2. The $AJ$-conjecture for a knot $K \subset S^3$ relates the $A$-polynomial and the colored Jones polynomial of $K$. If $K$ satisfies the $AJ$-conjecture, sufficient conditions on $K$ are given for the $(r,2)$-cable knot $C$ to also satisfy the $AJ$-conjecture. If a reduced alternating diagram of $K$ has $\eta_+$ positive crossings and $\eta_-$ negative crossings, then $C$ will satisfy the $AJ$-conjecture when $(r+4\eta_-)(r-4\eta_+)>0$ and the conditions of Theorem 2.2.1 are satisfied. Chapter 3 is about quantum curves and their relation to the $AJ$ conjecture. The variables $l$ and $m$ of the $A$-polynomial are quantized to operators that act on holomorphic functions. Motivated by a heuristic definition of the Jones polynomial from quantum physics, an annihilator of the Chern-Simons section of the Chern-Simons line bundle is found. For torus knots, it is shown that the annihilator matches with that of the colored Jones polynomial. In Chapter 4, a tangle functor is defined using semicyclic representations of the quantum group $U_q(sl_2)$. The semicyclic representations are deformations of the standard representation used to define Kashaev's invariant for a knot $K$ in $S^3$. It is shown that at certain roots of unity the semicyclic tangle functor recovers Kashaev's invariant.

In this paper, we examine Fox colorings of virtual knots, and moves called k-swap moves defined for virtual knot diagrams. The k-swap moves induce a one-to-one correspondence between colorings before and after the move, and can be used to reduce the number of virtual crossings. For the study of colorings, we characterize families of alternating virtual knots to generalize (2, n)-torus knots, alternating pretzel knots, and alternating 2-bridge knots. The k-swap moves are then applied to prove a "virtualization" of the Kauffman-Harary conjecture, originally stated for classical knot diagrams, for the above families of virtual pretzel knot diagrams.

Knot theory is the mathematical study of knots. In this thesis we study knots and one of its applications in DNA. Knot theory sits in the mathematical field of topology and naturally this is where the work begins. Topological concepts such as topological spaces, homeomorphisms, and homology are considered. Thereafter knot theory, and in particular, knot theoretical invariants are examined, aiming to provide insights into why it is difficult to answer the question "How can we tell knots appart?". In knot theory invariants such as the bracket polynomial, the Jones polynomial and tricolorability are considered as well as other helpful results like Seifert surfaces. Lastly knot theory is applied to DNA, where it will shed light on how certain enzymes interact with the genome.

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.