On Knots and DNA

Department of Mathematics, Linköping University

Mari Ahlquist

LiTH-MAT-EX–2017/17–SE

Credits: 16 hp
Level: G2
Supervisor: Milagros Izquierdo,
Department of Mathematics, Linköping University
Examiner: Göran Bergqvist,
Department of Mathematics, Linköping University
Linköping: December 2017
Abstract

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. There-
after 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 poly-
nomial, 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.

Keywords:
Knot theory, Topology, Homology, Jones polynomial, Bracket polynomial,
Tangles, DNA.

URL for electronic version:

http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-144294

Ahlquist, 2017. iii

Acknowledgements

There are many people I would like to thank. First of all my family. Throughout
my life they have always given me encouragement and love, and they have
believed in me even when I did not believe in myself.
To my supervisor Milagros Izquierdo I would like to say thank you for your
patience, support, feedback and guidance, and to my examiner Göran Bergqvist
I wish to express my gratitude for your thorough review which has ensured
the quality of this work. I am also thankful for all the valuable thoughts and
feedback given to me by my opponent Erik Bråmå on how to improve my work.
Last but "knot" least I wish to thank my boyfriend Kalle Trenter for his
understanding and unending support, as well as all of my friends and colleagues
for hours of interesting discussions.

Ahlquist, 2017. v
Nomenclature
Sn The n-sphere in Rm , n  m.
Bn The open n-ball Rn .
A The closure of a set A.
A⇥B The Cartesian product.
G'H Two isomorphic groups.
e
0 The Trivial group {0}.
Z The integers (infinite cyclic group).
Zn The cyclic group of order n.
X, Y Topological spaces.
X n, X N Finite and infinite product spaces.
hKi Kauffman polynomial of a link K.
(a, b) The open interval {x 2 R : a < x < b}.
[a, b] The closed interval {x 2 R : a  x  b}.
T̄ The usual topology on R.
T̂ The half-open topology on R.
A\B The (relative) complement {x 2 A :2 / B}.
f 1 (A) The preimage of a set A, i.e. {x 2 X : f (x) 2 A}.
X⇠ =Y Two homeomorphic spaces.
Int(A) The interior of a set A.
[z], z̄ The equivalence class of z.
Cn (K) The group of n-chains.
Zn (K) The group of n-cycles.
Bn (K) The group of n-boundaries.
Hn (K) The n:th homology group.
K A complex in homology and a knot in knot theory.
⌦ Equivalence of knot diagrams.

Ahlquist, 2017. vii

Contents

1 Introduction 1

2 Background 3
2.1 Algebra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2.1 Topological Spaces . . . . . . . . . . . . . . . . . . . . . . 7
2.2.2 Homeomorphisms . . . . . . . . . . . . . . . . . . . . . . . 15

3 Homology 21
3.1 Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.2 The Algebra of Chains . . . . . . . . . . . . . . . . . . . . . . . . 24
3.3 Homology Groups . . . . . . . . . . . . . . . . . . . . . . . . . . 28

4 Knot Theory 35
4.1 Introduction to Knot Theory . . . . . . . . . . . . . . . . . . . . 35
4.2 Prime Decomposition Theorem . . . . . . . . . . . . . . . . . . . 41
4.3 Bracket Polynomial . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.4 Jones Polynomial . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5 Tangles and DNA 49

5.1 Tangles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
5.2 DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Ahlquist, 2017. ix
List of Figures

2.1 Examples of homeomorphisms. . . . . . . . . . . . . . . . . . . . 7

2.2 Four examples of topologies from Example 2.2.6. . . . . . . . . . 9
2.3 Unit disk to hemisphere. . . . . . . . . . . . . . . . . . . . . . . . 11
2.4 Torus: S 1 ⇥ S 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.5 Möbius strip. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.6 Cantor set binary tree - by Sam Derbyshire [16]. . . . . . . . . . 17

3.1 Examples of simplexes. . . . . . . . . . . . . . . . . . . . . . . . . 22

3.2 Four surfaces: sphere, torus, Klein bottle, and projective plane. . 23
3.3 Orientations of 2-cells. . . . . . . . . . . . . . . . . . . . . . . . . 24
3.4 A complex on K2 . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.5 Boundaries of cells. . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.6 Complex K for Example 3.3.8. . . . . . . . . . . . . . . . . . . . 32

4.1 Figure 8 knot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

4.2 Knot table - by Wikipedia user Jkasd [22], published with per-
mission. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.3 Wild knot - by Wikipedia user Jkasd [21], published with permis-
sion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.4 Unknot in disguise. . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.5 Tricoloring of trefoil. . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.6 Positive and negative crossing. . . . . . . . . . . . . . . . . . . . 40
4.7 Seifert surface for 51 . . . . . . . . . . . . . . . . . . . . . . . . . . 42
4.8 Bracket polynomial for the Hopf link. . . . . . . . . . . . . . . . 44
4.9 Crossings for the skein relation . . . . . . . . . . . . . . . . . . . 47

5.1 Two examples of tangles. . . . . . . . . . . . . . . . . . . . . . . . 50

5.2 Numerator and denominator of a tangle. . . . . . . . . . . . . . . 50
5.3 Tangle sum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Ahlquist, 2017. xi
xii List of Figures

5.4 Exceptional tangles . . . . . . . . . . . . . . . . . . . . . . . . . . 51

5.5 Orientations of vertical and horizontal twists . . . . . . . . . . . 52
Chapter 1

Introduction

Knot theory is the mathematical theory of knots. At this stage, you can think of
a knot as a piece of string that you have tied and then glued the ends together.
At first glance it might seem like a very unusual mathematical field. Does it
really have any practical use? - Yes, it most certainly does! Knot theory can be
applied to several areas, one of them being in the study of DNA.
DNA is the genetic code of every living thing and biologists study it with the
purpose of better understanding life. Deeper knowledge about DNA would not
only give more information about evolution, but it would also make it possible
to find new and improved disease treatments. Because DNA is the instruction to
how we function it is involved in several processes, processes that aim to decode
or extract the information, or to improve or change the information. There
are also processes that focus on keeping the DNA "tidy" to ensure that other
processes work smoothly. The processes are conducted by enzymes. Enzymes
facilitate reactions; some break down the food we eat, some help decode the
genome and some are used in industry applications such as producing medicine.
One group of enzymes called recombinase manipulate the genome by genetic
recombinations. Recombinase can move one segment of DNA to another location
on the genome or it can insert alien DNA into the genome. The latter is a key
part of the life cycles of some viruses. Understanding the actions of some of
these enzymes can be achieved by combining biology with mathematics. Tangle
theory (a part of knot theory) can be used to understand how recombinase
enzymes interact with DNA. [1]
To utilize the theory of tangles, one must first build a good basis in knot
theory, looking for answers to questions like "What is a knot (mathematically)?"
and "How do we tell knots apart?". The first question may seem trivial but it
took some time before the definition of a knot was put on a firm mathematical

Ahlquist, 2017. 1
2 Chapter 1. Introduction

base. The second question is in fact one of the biggest unsolved questions
in the field. Today, many knots can be distinguished from one another but
there is still no invariant that can fully classify all knots. An invariant is a
property of an object that never changes. Invariants help us tell objects apart.
The invariant cannot change with the representation of the object but needs to
remain the same. There are many thing that can be an invariant, e.g. a number,
a polynomial, a group. Studying invariants will be a red thread throughout this
work, not only invariants for knots but also for more general objects such as
spaces.
The theory of knots is a subfield to the field known as topology. Topology
can be described as the study of which properties of objects are left unchanged
under continuous deformations. Topologists study ways to tell objects (often
spaces) apart, and knot theory utilizes many of the tools and techniques found
in topology.
This bachelor thesis will begin with a mathematical background, Chapter
2, that includes concepts from both algebra and topology. In the section on
topology homeomorphisms, a concept central to this work, is described. In
Chapter 3 the theory of homology is developed. Homology is a powerful tool
used to study the structure of spaces. After Chapter 3 we have gained enough
topological understanding to dive into Chapter 4: the theory of knots. This
chapter covers many concepts in knot theory, however, it is still just a taste of
all the wonders this field has to offer. This chapter is concluded by the Jones
polynomial, a strong invariant for knots. In the final chapter, Chapter 5, tangles
are described as well as some fantastic results they have given to the field of
DNA-research.
Chapter 2

Background

This chapter covers preliminary concepts needed for the rest of this thesis. Both
algebraic concepts (such as groups and rings) and topological concepts (such as
topological spaces, continuity and compactness) are described. A big part of
the section on topology are homeomorphisms, as they are essential to the rest
of this thesis.

2.1 Algebra
In this section we shall go through some important concepts in algebra. A good
account of algebraic concepts can be found in [18] and [11]. The key concept in
this section will be Polynomial rings.

Definition 2.1.1. A Group, denoted (G, ⇤), is a set of elements G together

with an operation ⇤, that satisfy the following properties

1. Associativity: ⇤ is associative, i.e. (x ⇤ y) ⇤ z = x ⇤ (y ⇤ z) for all elements

x, y, z 2 G.
2. Identity element: There exists a unique identity element, e 2 G s.t. e⇤x =
x ⇤ e = x for all x 2 G.
3. Inverse: For each element x 2 G exists an inverse x 1 s.t. x ⇤ x 1 =
x 1 ⇤ x = e.

Moreover, if the operation is commutative (x ⇤ y = y ⇤ x) then the group (G, ⇤)

is called an abelian group.

Example 2.1.2. The set Z of integers together with addition form a group,
(Z, +). Addition with integers is associative, it has the identity element 0, and

Ahlquist, 2017. 3
4 Chapter 2. Background

8x 2 Z, 9y 2 Z : x + y = 0, y is the inverse and can also be denoted x. (Z, +)

is abelian. N with addition is an simple example of a set that fails to be a group.

Definition 2.1.3. A group G is called cyclic if it can be generated by a single

element a, such that G = hai = {k ⇤ a : k 2 Z}.

Example 2.1.4. Z is a cyclic group Z = h1i = {1 ⇤ k : k 2 Z}.

The order of a finite group is the number of elements in the group. The
set of (positive) integers modulo n form the finite cyclic group Zn of order n.
The rank, rk(G), of a group G is the minimum number of generators needed
to generate G. For example Z ⇥ Z ⇥ Z = Z3 has rank 3, and every cyclic group
(e.g. Z6 ) has rank 1.

Definition 2.1.5. Let (G, ⇤G ), (H, ⇤H ) be groups. A homomorphism h : G !

H is a function such that 8g1 , g2 2 G it holds that h(g1 ⇤G g2 ) = h(g1 ) ⇤H h(g2 ).
An isomorphism is when we also require h to be a bijection. Two groups are
therefore called isomorphic, denoted G ' H if there is exists an isomorphism
between them.

Example 2.1.6. The most general abelian group is a product of cyclic groups,
finite or infinite, and can therefore be written as

Zr ⇥ Zn1 ⇥ ... ⇥ Znk

where r is the rank. This a actually a very powerful result called the Structure
Theorem and a proof can be found in [18].

From groups we now go on to create something called rings.

Definition 2.1.7. A Ring, denoted (R, +, ⇤), is a set of elements R together

with two operations + and ⇤, called addition and multiplication respectively,
that satisfy the following properties

1. (R, +) is an abelian group.

2. ⇤ is associative.
3. ⇤ is distributive over +, meaning that x ⇤ (by + z) = (x ⇤ y) + (x ⇤ z) and
(x + y) ⇤ z = (x ⇤ z) + (y ⇤ z) hold for all x, y, z 2 R.

If ⇤ is commutative we way that R is a commutative ring.

Example 2.1.8. Several of the most common sets of numbers Z, Q, R, C

together with normal addition and multiplication are rings. As is Mn (R), the
set of all n ⇥ n matrices, under normal matrix addition and multiplication.
2.1. Algebra 5

Now it is time to look at polynomial rings which basically are sets of

polynomials with coefficients from a ring. It is called a polynomial ring because
the set together with addition and multiplication will form a ring. Let’s be
precise.

Definition 2.1.9. Let R be a ring, then a polynomial p in x over R is a formal

sum
1
X
p(x) = a k xk
k=0

where ak 2 R for all k and all but a finite number of ak = 0. The set of all such
polynomials is denoted R[x].

The set of polynomials R[x] is a ring with addition and multiplications de-
fined as follows.
P1
Definition 2.1.10. P1 1. The sum of two polynomials, p1 (x) = k=0 ak x
k

and p2 (x) = k=0 bk x where ak , bk 2 R, is defined as

k

1
X
p1 (x) + p2 (x) = (ak + bk )xk .
k=0

2. The product of two polynomials p1 (x) and p2 (x) is defined as

1
X
p1 (x)p2 (x) = c k xk ,
k=0

Pk
where ck = j=0 a j bk j.

Looking at the definitions we see that addition and multiplication are done
in the same fashion that we are used to. We add term by term and we multiply
"crosswise".

Example 2.1.11. If Z6 is the set of integers modulo 6, with normal addition and
multiplication, modulo 6, the (Z6 , +, ⇤) forms a ring. Now, let p1 (x) = x2 +x+3
and p2 (x) = 2x + 4 be two polynomials in the ring Z6 [x], then

p1 (x) + p2 (x) = (x2 + x + 3) + (2x + 4) =

= x2 + (1 + 2)x + (3 + 4) =
= x2 + 3x + 1
6 Chapter 2. Background

and

p1 (x)p2 (x) = (x2 + x + 3)(2x + 4) =

= (1 ⇤ 2)x3 + (1 ⇤ 4 + 1 ⇤ 2)x2 + (1 ⇤ 4 + 3 ⇤ 2)x + (3 ⇤ 4) =
= 2x3 + 4x.

Definition 2.1.12. A field F is a commutative ring R with identity 1, in which

every nonzero element has a multiplicative inverse.
This means that if R is a field (R, ⇤) is an abelian group.
Definition 2.1.13. A Laurent polynomial with coefficients ai in a field F , is
the formal sum X
p(x) = ak xk , k 2 Z,
k

with finitely many of the coefficients nonzero.

Simply put, a Laurent polynomial is a polynomial for which we allow neg-
ative powers of x. We denote the collection of polynomials over the field F by
F [x, x 1 ]. F [x, x 1 ] is a ring.

2.2 Topology
There are many concepts in knot theory that most people intuitively can un-
derstand. This allows for interesting and easy introductions in popular science
(but oddly enough, most people are still unaware of knot theory). However,
in order to dive deeper into knot theory, to be able to fully understand it, we
first need to learn some topology. This section is meant to give readers who
have not taken a course in topology enough background to be able to follow and
understand the concepts of this thesis. We follow the books [2], [5], and [11] in
this section.
In topology we rid ourselves of the concepts of distance when determining if
two objects are near. Transforming spaces continuously is a cornerstone in this
thesis. If you, by using for example stretching and bending, can transform A
into B, and B into A, you can consider them to be the same, this is the notion
of homeomorphisms. Homeomorphisms give equivalence between spaces and we
wish to study properties that remain intact under homeomorphisms. We must
be very restrictive with operations such as cutting and pasting. Combinations
of these are often not continuous and can therefore yield non-homeomorphic
spaces. See Figure 2.1. To emphasize the concept of homeomorphism we begin
will the following definition.
2.2. Topology 7

Figure 2.1: Examples of homeomorphisms.

Definition 2.2.1. Let A and B be topological spaces. Then A is topologically

equivalent or homeomorphic to B if there is a continuous invertible function
f : A ! B with continuous inverse f 1 : B ! A. Such a function f is called a
homeomorphism.

We need more knowledge to fully grasp this definition. In the following

sections all needed concepts will be explained.

2.2.1 Topological Spaces

A topological space is a very general concept of a space. Later we will see
that metric spaces are specializations of topological spaces where the topology
is given by distances.

Basic concepts
Definition 2.2.2. A topological space is a set X with a collection B of collections
Bx , for all x 2 X, of nonempty subsets N ✓ X, called neighborhoods, such that

• every point is in some neighborhood, i.e.,

8x 2 X, 9N 2 Bx such that x 2 N

• the intersection of any two neighborhoods of a point contains a neighbor-

hood of the point, i.e.,

8N1 , N2 2 Bx , 9N3 2 Bx such that x 2 N3 ✓ N1 \ N2

8 Chapter 2. Background

• for every neighborhood N of a point there is a smaller neighborhood N0

such that each point in N0 has a neighborhood contained in N , i.e.,

for N 2 Bx , 9N0 2 Bx such that 8y 2 N0 there is some Vy 2 By with Vy ⇢ N.

The set Bx is called a neighborhood basis for x, and B = [Bx generate a

topology as follows: a subset O ✓ X is an open set if for each x 2 O, there is a
neighborhood N 2 B such that x 2 N and N ✓ O. The set T of all open sets is
a topology on the set X, and the set B is called a basis for the topology on X.

Remark. By this definition ; is always open.

For a set X with topology T we will use the notation (X, T) to refer to
the topological space. However, when there is no ambiguity, this notation will
sometimes be abused and X will stand for a topological space.
In the beginning of this section we mentioned that a metric space is a topo-
logical space, we shall now look at the Euclidean space.
Example 2.2.3. With the Euclidean distance metric in Rn ,
p
d(x, y) = (x1 y1 )2 + (x2 y2 )2 + ... + (xn yn )2 ,

we can form n-dimensional balls, B(x, r) = {y 2 Rn : d(x, y) < r} of radius

r > 0, around any point x. Together these balls form a basis B = {B(x, r) :
x 2 Rn , r > 0} for the topology on Rn .
More generally: If X is a set with a metric d (metric space), then the set
of balls B = {B(x, r), x 2 X, r > 0} is a basis for a topology on X, where
B(x, r) = {y 2 X : d(x, y) < r} for r > 0.

Example 2.2.4. For R we construct B = {(a, b) : x 2 R, a < x < b}, the set
of all open intervals on R. The topology T̄ given by B is called usual topology
on R. The open neighborhoods are (a, b).
The construction of topology above is equivalent to the topology in Theorem
2.2.5 that is stated below. This theorem can be taken as the definition of a
topology.
Theorem 2.2.5 (cf. [11]). T is a topology on X iff
1. X and ; are elements of T.
2. The union of any collection of elements in T is in T.
3. The intersection of any finite collection of elements in T is in T.

Theorem 2.2.5 gives a new way to determine if T is a topology on a set X.

2.2. Topology 9

Figure 2.2: Four examples of topologies from Example 2.2.6.

Example 2.2.6. Let X = {x, y, z} be three points. Four examples of topologies

on X can be found in Figure 2.2. They are (from left to right):
• T1 = {;, X},
• T2 = {;, {y}, {x, y}, X},
• T3 = {;, {x}, {y, z}, X}, and
• T4 = {;, {x}, {y}, {z}, {x, y}, {x, z}, {y, z}, X}.
Non of these topologies are homeomorphic to one another. The first one {;, X}
is called the trivial topology, and the last one is called the discrete topology on
X. There are several more topologies on X - simply find other combinations of
subsets that satisfy Theorem 2.2.5.

Definition 2.2.7. Let C be a subset of a topological space X with topology T,

then we say that C is closed if X \ C is open.
Example 2.2.8. Let X = {x, y, z}, T = {;, {y}, {x, y}, {y, z}, X}, C1 = {x}
and C2 = {x, y}. Are C1 and C2 closed? Well, C1 is closed if the complement is
open (i.e. X \ C1 ✓ T). X \ C1 = {y, z} ✓ T so X \ C1 is open and C1 is closed.
Similarly, X \ C2 = {z} 6✓ T so X \ C2 is not open and therefore C2 cannot be
closed.
Open and closed sets depend on our choice of basis and topology. Changing
them may change which sets we consider to be open and closed - altering all
concepts that in turn depend on these, such as, compactness and continuity.
This makes things a little abstract. For instance, the trivial topology has
only one neighborhood N = X. ; and X are, by definition, the only open and
the only closed sets.
From the definition of neighborhoods we get that they can be any non-empty
set, so one neighborhood of the point x could be {x}. For the discrete topology
we have that any subset of X is both open and closed.
For R the standard neighborhoods are the open intervals (a, b) and the usual
topology is the set of all of these open intervals, as seen in Example 2.2.4. On
R there is a different, very interesting, topology called the half-open topology.
10 Chapter 2. Background

Example 2.2.9. Let the interval [a,b) with a, b 2 R, be a neighborhood 8x 2

[a, b). There is a topology T̂ on R where set of intervals B = {[a, b)} form a
basis for T̂. T̂ is called the half-open topology. The interval [1, 2) will be a
neighborhood for the point 1, and is by definition an open set. Furthermore
this half-open topology is fundamentally different form the usual topology with
open neighborhoods (a, b), because there is no interval of the form (a, b) that is
a neighborhood of 1 and also a subset of [1, 2).
The following definition gives us a property that makes spaces nice and
informative to study.
Definition 2.2.10. A topological space is Hausdorff if, for any two distinct
points in X, there are disjoint open sets, one containing one of the points, the
other containing the other.
That a space is Hausdorff is a good property to have. It means that we can
study each point individually, it is not hidden in a cluster of points. All spaces
we will be working with are Hausdorff. In numerical analysis if you consider
a situation where you have data from real numbers and an error margin, the
resulting space will not be Hausdorff. Computers only allow a finite (in many
cases fixed) number of decimals, and hence does not save enough information
to study every point in R individually. There are several intervals in which you
cannot tell points apart. This problem is common in real applications on data
sets.
Example 2.2.11. Both (R, T̄) and (R, T̂) are Hausdorff.
Example 2.2.12. In Example 2.2.6 only T4 is Hausdorff. In T3 , for example,
we can never study just the point z, we must always consider y and z together.
From a topological space (X, T) we can create a new space by taking a subset
A of X and using T to induce a topology on A. The following definition explains
how.
Definition 2.2.13. Let X be a topological space with topology T and let A ✓
X. A neighborhood of a point x 2 A relative to A is of the form N \ A where N
is a neighborhood of x in X. The topology TA generated by this basis is called
the subspace topology on A induced by the topology T on X.
From any topological space we can make new subspaces by using this method-
ology. The neighborhoods in the subspace topology (N \ A) are open relative
to A, but not necessarily open relative to X. For the Euclidean space with the
normal topology (see Example 2.2.3) we can take any subset and induce a sub-
space topology. For some subsets (e.g. closed ones) there will be neighborhoods
in the subspace topology that are not a part of the normal topology.
2.2. Topology 11

Figure 2.3: Unit disk to hemisphere.

Continuity, Connectedness & Compactness

Continuity is an important concept in many areas of mathematics and topology
is the right setting for studying it. Several things depend on continuity, but first
things first, we begin with the definition.

Definition 2.2.14. Let (X, TX ) and (Y, TY ) be topological spaces. A function

f : X ! Y is continuous if for every A 2 TY , f 1 (A) 2 TX .

This is equivalent to saying that for each x 2 X, given a neighborhood Nf (x)

in TY , there is a neighborhood NX in TX such that x 2 NX which belongs to
the preimage of Nf (x) . The inverse is given by f 1 (A) = {x 2 X : f (x) 2 A}.
Remark. We do not require f 1
to be a function, and in general, it is usually
not one.

Example 2.2.15. The function f : R2 \ {(0, 0)} ! S1 , given by f (x) = kxk ,

x

is continuous. The inverse of f does not exist.

Example 2.2.16. Let f be a vertical projection from the open

p unit disk to the
open hemisphere, see Figure 2.3. Then f : (x, y) ! (x, y, 1 x2 y 2 ), is a
continuous function, as is f 1 .

Leaving continuity, our next step is connectedness. It is quite intuitive what

connectedness is: connected spaces are in some sense "stuck together" - we could
say that from any point in the set you can reach any other without ever leaving
the set.

Definition 2.2.17. A topological space X is connected if X cannot be written

as a union of two non-empty disjoint open sets.
12 Chapter 2. Background

We need to take care when applying this definition. All possible divisions
of the space must be considered otherwise there is a possibility that a "gap" is
hidden in one of the two open sets.

Example 2.2.18. The open interval ( 1, 1) is connected, as is the torus (Figure

2.4), the sphere and the ball.

Example 2.2.19. (R, T̄) is connected but (R, T̂) is not since the latter can be
written as the disjoint union ( 1, 0) [ [0, 1).

The following theorem ties together the concepts of continuity and connect-
edness.

Theorem 2.2.20 (cf. [11]). Let X and Y be topological spaces and f : X ! Y

a continuous function onto Y. If X is connected, then Y is connected.

Definition 2.2.21. Let A be a subset of a topological space X. An open cover

of A is a collection O of open subsets of X so that A lies in the union of the
elements of O, i.e.,
[
A✓ O
O2O

A subcover of O is a collection O ✓ O so that A lies in the union of the elements

0

in O0 . A finite cover (or subcover) is a cover O consisting of finitely many sets.

Definition 2.2.22. A topological space X is compact if every open cover of X

has a finite subcover.

Example 2.2.23. The n-sphere is compact for n 2 N. Any finite topological

space is compact, such as the spaces in Example 2.2.6.

Example 2.2.24. An infinite set with the discrete topology is not compact.

To conclude this part we will state two theorems concerning the compact-
ness of subsets, and the connection between continuous functions and compact
spaces. Thereafter we will move on to new ways of constructing spaces by using
products and quotients.

Theorem 2.2.25 (cf. [11]). If X is a compact topological space and A is a

closed subset of X then A is compact.

Theorem 2.2.26 (cf. [11]). Let X be a compact topological space and f : X !

Y a continuous function from X onto a topological space Y . Then Y is compact.
2.2. Topology 13

Figure 2.4: Torus: S 1 ⇥ S 1 .

Product & Quotient Spaces

This subsection starts by looking at the product of spaces and then it moves on
to the quotients of spaces. The reader will have used the concept of a product
space many times but perhaps without calling it so. For instance, R3 is the
(Cartesian) product R ⇥ R ⇥ R. By taking the product of spaces we can create
new, interesting, topological spaces for us to study.
Definition 2.2.27. Let X be a topological space with topology T and Y a
topological space with topology T 0 . A basis for the product topology on X ⇥ Y
is given by B where N 2 B if N is on the form N = O ⇥ O0 for O 2 T and
O0 2 T 0 . Projection functions pX : X ⇥ Y ! X and pY : X ⇥ Y ! Y are
defined by

pX (x, y) = x
pY (x, y) = y.

pX and pY are continuous and X ⇥ Y is called a product space.

Example 2.2.28. If we take a circle, S 1 and an interval [a, b] ⇢ R, the product
will be a closed cylinder. The product of two circles, S 1 ⇥ S 1 , is a torus (see
Figure 2.4).
Q
For product spaces in general we have that for given X = Xi and fi :
X ! Xi , the product topology is the minimal topology on X that makes all
fi continuous. Two valuable results about product spaces are that the prod-
uct of connected topological spaces is connected, and the product of compact
topological spaces is compact.
With product spaces and continuity we can study continuous deformation
from one function to another. Imagine the function f0 (x) = 2sin(x), if you
continuously increase the amplitude you could obtain the function f1 (x) =
14 Chapter 2. Background

10sin(x). We say that two functions are homotopic if one can be continuously
transformed into the other. Formally we take the following definition.

Definition 2.2.29. Let X and Y be topological spaces and I = [0, 1]. Then
H : X ⇥ I ! Y , given by H(x, t) = Ht (x) for x 2 X and t 2 I, is a
homotopy between the continuous functions f0 : X ! Y and f1 : X ! Y if
H continuous and satisfies

H(x, 0) = f0
H(x, 1) = f1 .

Remark. It is important that the reader observes the fact that all Ht (x) are
required to be continuous for t 2 I.

Example 2.2.30. In topology one usually talks about spaces being "elastic",
we can now describe stretching in terms of homotopy. Take R2 and stretch it
out so that each point is sent twice as far away from origo. We can construct a
continuous function H : R2 ⇥ I ! R2 given by

H(x, 0) = H0 (x) = x
H(x, t) = Ht (x) = (1 + t)x
H(x, 1) = H1 (x) = 2x.

H is a homotopy between H0 and H1 .

Now we move on to quotient spaces. Similarly to product spaces, quotient

spaces will yield new spaces for us to study. They occur when we identify (or
glue together) certain points in a space. If you would, for example, take the
boundary of a disk to a single point (without shrinking the surface area), the
result will be a sphere. We start with the definition of a quotient topology
before we define a quotient space (also known identification space).

Definition 2.2.31. Let (X, T) be a topological space and let f : X ! Y be

a function onto the set Y . Define the quotient topology T 0 on Y by defining
U ✓ Y to be open in Y if

U 2 T 0 iff f 1
(U ) 2 T

Remark. There is no demand for an initial topological structure on Y.

2.2. Topology 15

Instead of specifying a function that satisfies Definition 2.2.31 one can simply
specify just the points that should be glued together according to an equivalence
relation - saying that the points that are glued are equivalent.
Example 2.2.32. Take a rectangle and imagine gluing two of the opposite sides
together to form a cylinder. This is the same as saying that the points on one
edge are equivalent to those on the other.
Example 2.2.33. Let X be a topological space with ⇠ an equivalence relation
defined on X. The equivalence class of x 2 X is given by

[x] = {y 2 X : y ⇠ x},

and the identification space X/ ⇠ is the set of equivalence classes of the relation
⇠, equipped with the quotient topology:

X/ ⇠ = {[x] : x 2 X}.

The topology on X induces a topology in X/ ⇠. This is the quotient topology

from Definition 2.2.31.
Example 2.2.34. To formalize Example 2.2.32; let X = {(x, y) : 0  x 
1, 0  y  1} and form the equivalence classes
(
{(x, y)} if x 6= 0, 1 and 0  y  1,
[(x, y)] =
(0, y) ⇠ (1, y) if x = 0, 1 and 0  y  1.

Then X/ ⇠ becomes the cylinder.

2.2.2 Homeomorphisms
Now we shall look at an updated version of the definition of homeomorphisms
that was discussed in the beginning. Homeomorphisms gives us topologically
equivalent spaces. It is thanks to the following definition that we can bend and
stretch spaces and still view them as "the same space".
Definition 2.2.35. A function f , between topological spaces X and Y , is a
homeomorphism if f is continuous and invertible and the inverse function f 1
is also continuous. The spaces X and Y are then topologically equivalent, also
called homeomorphic, denoted X ⇠ =Y.
The examples in Figure 2.1 are homeomorphic. Other examples are stretch-
ing one open interval in R to any other, and the very famous one of the torus
which is homeomorphic to a coffee mug.
16 Chapter 2. Background

Homeomorphisms help us find unique properties that remain unchanged

when during a continuous transformation. These properties lie "deeper" in
the structure of the spaces and are therefore interesting to study. What char-
acteristics can be found and how can two spaces be differentiated from one
another?
Example 2.2.36. The stereographic projection S : S3 \ {N } ! R3 is a home-
P4
omorphism. Therefore the 3-dimensional sphere ( i=1 x2i = 1) minus the north
pole, is the same space as R3 .
Make the projection by sending a point P = (x1 , x2 , x3 , x4 ) on the sphere
to a point P 0 = (x, y, z, 0) 2 R3 as follows: draw a line from the north pole
N = (0, 0, 0, 1) of the sphere through P . This line is given by

(t) = (0, 0, 0, 1) + (x1 , x2 , x3 , x4 1)t

and it intersects R3 when 0 = 1 + (x4 1)t () t = (1 x4 ) 1

. S can now be
written as
⇣ x x2 x3 ⌘
1 1
S(P ) = ((1 x4 ) )= , , .
1 x4 1 x4 1 x4
S is continuous, invertible and has a continuous inverse given by
⇣ 2x 2y 2z µ 1 ⌘
S 1 (P 0 ) = , , , , where µ = x2 + y 2 + z 2 .
µ+1 µ+1 µ+1 µ+1

S is therefore a homeomorphism, and S3 /{N } ⇠

= R3 .

(a) Rectangle (b) Twist (c) One half twist (d) Three half twists

Figure 2.5: Möbius strip.

Example 2.2.37. This example is taken from Armstrong’s book Basic Topol-
ogy [2]. It is meant to illustrate that homeomorphisms are more than just
stretching and bending. Hence, we cannot only think about topological spaces
as being made of rubber. To, for example, construct a Möbius Strip, one starts
with a rectangle that has 2 directed edges, as in Figure 2.5a, then identify the
edges along the specified direction. In order to do so we induce a half twist,
2.2. Topology 17

Figure 2.6: Cantor set binary tree - by Sam Derbyshire [16].

Figure 2.5b and 2.5c. However, nothing stops us from adding more twists. As
long as we identify the edges according to the directions the same points on
both edges will be made to coincide. This always gives an odd number of half
twists. So all sub-figures in Figure 2.5 are homeomorphic.

Example 2.2.38. The famous Cantor set is constructed by iteratively removing

the open middle third of line segments. Start with A0 = [0, 1], which is compact,
remove the middle third and obtain A1 = [0, 13 ] [ [ 23 , 1], which also is compact.
Again, remove the middle thirds and obtain A2 = [0, 312 ] [ [ 322 , 332 ] [ [ 362 , 372 ] [
[ 382 , 1]. Repeating this process gives

3n [
1
1 ✓  ◆
3j 3j + 1 3j + 2 3j + 3
An = , [ , , for n 1.
j=0
3n 3n 3n 3n

The Cantor set, defined as

1
\
C := An ,
n=1

is a compact set. Look at Figure 2.6, in black we can see the first steps (A0
to A5 ) in the construction of C. In red we can see a binary tree forming. In
fact: each point in the Cantor set is determined by a unique (infinite) binary
sequence. This means that there is a bijection from C to all infinite binary
sequences.
Let 2 denote the topological space {0, 1} with the discrete topology. From
this we can create the space

2N = {(xn ) : xn 2 {0, 1}, n 2 N},

18 Chapter 2. Background

of all infinite binary sequences with the product topology of the discrete topology
in {0, 1}. By choosing 0 to represent the left interval and 1 to represent the right
interval in each step of the Cantor set construction we can form a sequence
(represented by the binary tree shown in Figure 2.6) that can uniquely lead us
to a point in C. It sounds plausible that 2N is homeomorphic to C, which in
fact it is. To prove this it is common in the literature to take the route through
ternary expansions, but there is an approach closer to the material in this thesis
which uses binary expansion and the Cantor Intersection Theorem to construct
a homeomorphism between C and 2N . The reader is referred to Landstedt’s
publication [12] for the details.

Concepts Depending on Homeomorphisms

The reader will notice that almost everything from now on will depend on
homeomorphisms. Homeomorphisms are the foundation for the next chapter on
homology, as well as the basis for the entire study of knots. Even so, this chapter
will end with a few key concepts that are directly dependent on homeomorphic
functions.
Homotopy has previously been defined (Definition 2.2.29) and an example of
a dilation of R2 was given. If we put an additional requirement on the functions
we get the following definition.

Definition 2.2.39. Let X and Y be topological spaces. A function H : X ⇥

I ! Y is an isotopy if H is a homotopy and each Ht (x) is a homeomorphism.

Demanding homeomorphic functions means that we not only need contin-

uous functions (as for homotopy) but also continuous inverses. Again, looking
back to Example 2.2.30. Stretching R2 has a logical inverse in shrinking it. It
is common that to take Ĥ0 = Id (the identity).

Example 2.2.40. From Example 2.2.30 we have a homotopy H : R2 ⇥I ! R2 .

We can construct the following function for x 2 R2 and t 2 I: Ĥ : R2 ⇥I ! R2 ,
where

H0 (x) = x Ĥ0 (x) = x

2 t
Ht (x) = (1 + t)x Ĥt (x) = x
2
1
H1 (x) = 2x Ĥ1 (x) = x.
2

All Ĥt are homeomorphisms, thus Ĥ is an isotopy between Ĥ0 = Id and Ĥ1 .
2.2. Topology 19

Definition 2.2.41. If f : X ! Y is a one-to-one map, and if f : X ! f (X)

is a homeomorphism when we give f (X) the induced topology from Y , we call
f an embedding of X in Y .

Definition 2.2.42. An n-dimensional manifold (or n-manifold) is a topological

space such that every point has a neighborhood homeomorphic to an open n-ball
in Rn .
Definition 2.2.43. An n-manifold with boundary is a topological space such
that every point has a neighborhood homeomorphic
P to either an open n-ball in
Rn or half of an open n-ball: {x 2 Rn : xi < 1, x1 0}.
By surface we will mean a 2-manifold. Surfaces with boundary will be an
important part of our study of knots later, but for now we will just give a few
examples. Boundary basically means that if you travel along the space you can
come to a verge where you can "fall off" if you cross it.

Example 2.2.44. The sphere, torus, Klein bottle and the projective plane are
all 2-manifolds. The punctured sphere (disk), punctured torus, a sheet of paper,
and the Möbius band are 2-manifolds with boundary.
Chapter 3

Homology

In this chapter we will take a different approach - to study building blocks that
together make up spaces. These blocks are called cells and cells can be glued
together to form complexes. The essence of this chapter is to create algebraic
structures that can help us distinguish different objects (spaces) from each other
by identifying properties that are unique to each object. This chapter follows
the excellent books of Armstrong [2], Fulton [5], and Kinsey [11].

3.1 Complexes
Definition 3.1.1. An n-cell is a is a set whose interior Int( ) is homeomor-
phic to an open ball, with the additional property that its boundary must be
divided into a finite number of lower-dimensional cells, called the faces of the
n-cell. We write ⌧ < if ⌧ is a face of .
Example 3.1.2. For this example we will restrict ourselves to cells called sim-
plexes, these are n-dimensional generalizations of triangles, see Figure 3.1.

1. A 0-simplex is a point A.
2. A 1-simplex is a line segment a = AB, and A < a, B < a.
3. A 2-simplex is a triangle, such as = ABC, and then AB, BC, AC < .
Note that A < AB < , so A < .
4. A 3-cell is a tetrahedron, with triangles, edges, and vertices as faces.

Connecting back to all cells, notice from the definition that there are no
requirements for a 1-cell to be a straight line, it suffices that its interior is

Ahlquist, 2017. 21
22 Chapter 3. Homology

a
A A B
(a) 0-simplex (b) 1-simplex
A
A

B
D
C B C
(c) 2-simplex (d) 3-simplex

Figure 3.1: Examples of simplexes.

homeomorphic to ( 1, 1). A 2-cell is not necessarily a triangle rather its interior

will be homeomorphic to an open 2-dimensional disk, and similarly for any n-
cells.
The faces of an n-cell are cells of lower dimension. With these cells one can
construct new objects: e.g., take a point, 0-cell, attach a 1-cell (string) to the
point so it forms a loop, and then attach a 2-cell (surface) to the string. This
might look a like flat disk with a marked edge and a point on the edge. This
type of construction forms something called a complex - a union of cells that
follow certain rules.
Definition 3.1.3. A complex K is a finite set of cells,
[
K = { : is a cell}

such that:
1. if is a cell in K, then all faces if are elements of K;
2. if and ⌧ are cells in K, then Int( ) \ Int(⌧ ) = ;.
The dimension of K is the dimension of its highest-dimensional cell.
Remark. The second rule in the definition stops cells from overlapping or cross-
ing each other. Cells can only meet at their boundary, i.e. they can share
faces.
If a complex is constructed using only simplexes (the very nice cells that
were shown in Example 3.1.2), we call it a simplicial complex. Simplexes usually
make calculations more straightforward but also more tedious. Even if they are
special cases of cells one does not lose any information when using them [6], and
they are therefore very common in the literature.
3.1. Complexes 23

Example 3.1.4. With a point, two strings and a rubber sheet you can make a
torus. Start with the 0-cell, then attach the end of the strings (1-cells) to the
point, forming two loops. Finally, bend and stretch the rubber sheet to align
the edges of the sheet with the loops, see Figure 2.4.

Instead of giving instructions for how each cell should be glued together
to form a complex we will represent complexes though planar diagrams. This
means that we take a 2-dimensional disk and mark which cells are supposed to
be glued together, as the examples in Figure 3.2. These show the four ways of
gluing the sides of a square to form a surface, (a) the sphere, (b) the torus, (c)
the Klein bottle, and (d) the projective plane.

a b b b
P Q P P P P P Q

a b a a a a a a

Q R P P P P Q P
b b b b
(a) S2 (b) T2 (c) K2 (d) P2

Figure 3.2: Four surfaces: sphere, torus, Klein bottle, and projective plane.

Definition 3.1.5. The space underlying a complex K, or the realization of K,

is the set of all points in the cells of K;

|K| = {x : x 2 2 K, a cell in K},

where x belongs to any ambient space.

So, what is the difference between a complex and a space? Well, a complex
is a set of cells of various dimensions, while a space is a set of points. This
means that |K| is a space and K are the building blocks of that space.
There are many different ways to assign a complex to a space. Therefore,
in examples we will not give a complex its own name (i.e. K) but rather use
the notation of the space (i.e. S2 ) to mean the complex on that space. This
is to emphasize that it is the structure of the space |K| and not the complex
itself that is important. By n-complex we will mean a complex K with cells of
dimension n or lower, e.g. a 2-complex can only consist of 0-, 1-, and 2-cells.
The following definition is a special case of a complex, namely a simplicial
complex on a surface consisting of only 2-simplexes.
24 Chapter 3. Homology

Definition 3.1.6. A surface (with or without boundary) is triangulable if a

simplicial 2-complex K can be found with X = |K| and the 2-simplexes (or tri-
angles) of K satisfy the additional property that any two triangles are identified
along a single edge or a single vertex or are disjoint.
This definition deals with surfaces we divide into (or construct by) triangles
(2-simplexes). We call these surfaces triangulable and we will base some of our
study of knots on surfaces with this property.

3.2 The Algebra of Chains

In the previous section we gave 1-cells directions to elucidate which sides to
glue together in the planar diagrams. Now we will use the fact that all cells
can be given a orientation, see Figure 3.3, to form what is known as directed
complexes.

Figure 3.3: Orientations of 2-cells.

Giving a cell an orientation is the equivalent of saying if one is using the right-
handed or the left-handed orientation of the basis in Euclidean three-space.
Definition 3.2.1. An n-cell is oriented if it has been assigned one of the two
orientations: positive ( ) or negative ( ).
The choice of which orientation is positive and negative is arbitrary. The
orientation of an n-cell induces an orientation on its faces.
Definition 3.2.2. An n-complex is directed if all cells of dimension 1 or higher
have been given an orientation.
Example 3.2.3. A 2-complex K is directed if each edge or 1-cell is given an
orientation (from initial to terminal point) and each polygon or 2-cell is given
an orientation (clockwise or counterclockwise).
In a directed complex the choice of orientation of the cells is arbitrary. It
serves as a basis for calculations. If two cells share a face and the orientation of
cells match up, the face can be removed without affecting the complex because
3.2. The Algebra of Chains 25

the cells induce opposite directions on the face and therefore cancel its influence.
We say that the cells are oriented in a compatible manner. Compare the complex
on the Klein bottle in Figure 3.2c with the one in Figure 3.4. The extra structure
(c, d, and e) makes no real difference and can be added and removed at will
because the orientations of the 2-cells are compatible (they induce opposite
orientation on the edges c, d, and e). If all adjacent cells in a complex have
compatible orientation we call the underlying space orientable.
Example 3.2.4. A surface is orientable when it is 2-sided, like the sphere and
torus but unlike the Möbius strip and the Klein bottle. We will return to the
concept of orientable surfaces in the chapter about knot theory.
Definition 3.2.5. Let K be a directed complex. An (integral) k-chain C in K
is a formal sum
C = a1 1 + a2 2 + ... + an n
where 1, are k-cells in K and a1 , a2 , ..., an are integers. Define 0 = 0.
2 , ..., n
Pn Pn
Definition 3.2.6. Let C = i=1 ai i and D i=1 bi i be k-chains in a directed
complex K. The sum C + D is defined by

C + D = (a1 + b1 ) 1 + (a2 + b2 ) 2 + ... + (an + bn ) n.

Remark. In addition to this definition we need to specify that 0 is a k-chain for

each value of k.
This is a very intuitive definition, but a short example is in order. Let
C = d + 2e and D = 3c 2d + e be q-chains in a directed complex, then

C + D = (d + 2e) + (3c 2d + e) = 3c d + 3e.

This definition, addition of k-chains, have the normal properties one usually
associates with addition; commutativity, associativity and the existence of both
identity and inverse. One adds chains of the same dimension.
Definition 3.2.7. Let K be a directed complex. Denote the group of all k-
chains on K, with addition, by Ck (K), k = 0, 1, ..., dim(K).
Ck (K) is the kth chain group of K. Ck (K) is an abelian group: the addition
satisfies the definition and all chains in Ck (K) are k-dimensional so adding them
will only yield new k-chains. Ck (K) is generated by the oriented k-cells of K.
If K is a finite complex, Ck (K) will be the free abelian group isomorphic Zn ,
for some n.
The following examples specify all chain groups for two different complexes,
one on the sphere and the other on the Klein bottle.
26 Chapter 3. Homology

Example 3.2.8. Look at the complex on the sphere in Figure 3.2. The 2-cell
has no given name or orientation, call it and give it the clockwise orientation.
Denote the whole complex K. Now we can calculate all the chain groups. The
complex is constructed from three 0-cell: P, Q, and R, two 1-cells: a and b, and
one 2-cell: . C0 is the group of all 0-chains on S2 . That means that all linear
combinations of P, Q and R are, such as 3P + 2Q R, belong to C0 .

C0 (S2 ) = {n1 P + n2 Q + n3 R : ni 2 Z} = hP, Q, Ri ' Z Z Z = Z3

C1 (S2 ) = {;, a, a, ..., b, b, ..., a + b, a b, 3a + 4b, ...} =
= {n1 a + n2 b : ni 2 Z} = ha, bi ' Z Z = Z2
C2 (S2 ) = {n : n 2 Z} ' Z

Example 3.2.9. Look at the complex on the Klein bottle shown in Figure 3.4.
It has two 0-cells: {P, Q}, five 1-cells: {a, b, c, d, e}, and three 2-cells: { , ⌧, ⇢}.

C0 (K2 ) = {a1 P + a2 Q : ai 2 Z} ' Z2

C1 (K2 ) = {a1 a + a2 b + a3 c + a4 d + a5 e : ai 2 Z} ' Z5
C2 (K2 ) = {a1 + a2 ⌧ + a3 ⇢ : ai 2 Z} ' Z3

b
P P
⇢ d
a Q a
c
⌧ e
P P
b

Figure 3.4: A complex on K2 .

Definition 3.2.10. The boundary of a k-cell , denoted @( ), is the (k 1)-

chain consisting of all the (k 1)-cells that are faces of , with orientation
inherited from the orientation of .
Figure 3.5 shows some examples of boundaries for different k-cells. For a 0-
cell P we define the boundary, @(P ) = 0. For the directed 1-cell b the boundary
is defined as the terminal point minus the initial point, i.e., @(b) = Q P . The
last one, 3.5(c), is an oriented 2-cell , whose boundary is a chain of 1-cells.
The 1-cells a, b and c are positive if their directions are consistent with ’s and
negative if not. Hence, for 3.5(c), we get the boundary @( ) = a b + c
3.2. The Algebra of Chains 27

a c
b
P P Q

b
(a) @(P ) = 0 (b) @(b) = Q P. (c) @( ) = a b + c.

Figure 3.5: Boundaries of cells.

Definition 3.2.11. Let C be a k-chain, C = a1 1 + a2 2 + ... + am m. The

boundary of C is

@k (C) = a1 @( 1) + a2 @( 2) + ... + am @( m ).

So, @k is a function that takes a k-chain and returns a (k 1)-chain, @k :

Ck (K) ! Ck 1 (K). The boundary function @k P is a homomorphism, Pnsince, if
n
C and D are both k-chains, then @k (C + D) = @k ( i=1 (ai + bi ) i ) = i=1 (ai +
bi )@k ( i ).
Example 3.2.12. Let C be the 2-chain 2⌧ 3⇢ from the complex in Figure
3.4. Then the boundary of C is

@2 (C) = 2@(⌧ ) 3@(⇢) = 2(b c + e) 3(b + c + d a) = 3a b 5c 3d + 2e.

Can we conclude something from this 1-chain that is the boundary? In this
particular case there is not much to say, however, there is a special case when
this boundary function gives rise to something interesting. Take another look at
Figure 3.4. The boundary of b is P P = 0. The same is true for @(a d e) = 0.
So, what does it mean when the boundary terms of a chain cancel out? Well,
it means that we have found a cycle!
Definition 3.2.13. If C is a k-chain in a directed complex K s.t. @k (C) = 0,
we say that C is a k-cycle. The set of all k-cycles in K, Zk (K), is a subgroup
of Ck (K).
Remark. Zk (K) is also the kernel of @k : Ck (K) ! Ck 1 (K).

Definition 3.2.14. If C is a k-cycle in a directed complex K such that there

exists a (k + 1)-chain D with @k+1 (D) = C, we say C is a k-boundary. The set
of all k-boundaries in K is Bk (K) ✓ Ck (K).
Remark. It is also the image of @k+1 : Ck+1 (K) ! Ck (K).
28 Chapter 3. Homology

Not only is Bk (K) a subgroup to Ck (K) in fact it is true that Bk (K) ✓

Zk (K) ✓ Ck (K). This is a consequence of the following theorem.
Theorem 3.2.15 (cf. [2]). The composition @k+1 @k : Ck+1 ! Ck 1 is the
zero homeomorphism.
If you apply the boundary function twice you will always get 0. A proof can
be found in [2], but in short this means the the boundary of any cell is a cycle.
Example 3.2.16. Let us revisit Figure 3.4 again. In this complex, name the
1-cycle a d e = C1 . The definitions says that because the boundary of the
2-chain D1 = is precisely C1 , then C1 is called a 1-boundary. The chains
C2 = b c + e and C3 = b + c + d a are also 1-boundaries with D2 = ⌧ and
D3 = ⇢ respectively. There exists no 2-boundaries because the complex contains
no 3-cells.

3.3 Homology Groups

In this section we will reach our goal for this chapter - Homology groups. Their
definition will be stated first and this whole chapter will be concluded by several
examples that give a deeper understanding as well as illustrate why all of this
has been worth doing, but first a short recap.
We have constructed chains from cells of the same dimension. On these
chains we have defined orientation and boundary and noticed that chains with
null-boundary form some kind of loop that we can think of as enclosing a k-
dimensional hole. By studying sets of cycles we will distinguish spaces based
on what type of cavities they have. For example, the normal sphere encloses a
3-dimensional cavity, as does the torus, but when we at the end of this section
look at the combined picture, over all dimensions, we will be able to tell them
apart. Homology groups Hk (K) are used to describe structures in different
dimensions. One can think of them as follows:

H0 (K) describes the connectivity of the components,

H1 (K) describes non-trivial loops, i.e. holes that look like a circle,
H2 (K) describes holes which look like a sphere,
..
.

Definition 3.3.1. Let K be a directed complex. The kth homology group of

K is Hk (K) = Zk (K)/Bk (K) = h ¯k , k 2 Zi, the group of equivalence classes
of elements of Zk (K) with the homology relation. In other words, Hk (K) is
Zk (K) with homology used instead of equality.
3.3. Homology Groups 29

Remark. A general rule for calculating Hk (K) is that we take the generators
from Zk (K) and then the relations from Bk (K)
In this part we denote the equivalence class of as ¯ as this will make the
calculations look tidier. The equivalence relation on chains is the following.
Definition 3.3.2. The k-chains C1 and C2 are homologous, written C1 ⇠ C2 ,
if C1 C2 2 Bk (K); i.e., if C1 C2 = @(D) for some (k + 1)-chain D.
Example 3.3.3. From Figure 3.5b, c: @(b) = Q P () P ⇠ Q therefor Q is
in P̄ , and @( ) = a b + c () a + c ⇠ b, so a + c 2 b̄.
Example 3.3.4. A few examples from Figure 3.4:
• @(a) = P P () P ⇠ P , naturally,
• @(c) = Q P () Q ⇠ P ,
• @(⌧ ) = b + e c () b + e ⇠ c, or b + e 2 c̄ and
• @(⇢) = b a + c + d () a b ⇠ c + d () a ¯ d.
b2c+
Theorem 3.3.5 (cf. [11]). Let K be a complex, with C1 , C2 , C3 , C4 chains in
Ck (K):
1. C1 ⇠ C2 .
2. If C1 ⇠ C2 , then C2 ⇠ C1 .
3. If C1 ⇠ C2 and C2 ⇠ C3 , then C1 ⇠ C3 .
4. If C1 ⇠ C2 and C3 ⇠ C4 , then C1 + C3 ⇠ C2 + C4 .
Remark. This theorem shows that homology is an equivalence relation and that
it works well with the chain addition (4).
Below are step-by-step directions for how to compute Hk (K). These seem
tedious and take a bit of practice to get the hang of. A reminder about notation:
e
the trivial group is denoted by 0.

Step-by-step Directions. First label and indicate orientation of all cells of

the complex. Do the computations for one dimension at a time, starting with
the highest.
1. Find Ck (K), the group of all k-chains.
2. For each generating k-chain C from (1), compute @(C).
3. Find Zk (K), using your computations from (2).
e then Hk (K) = 0.
(a) Note that if Zk (K) = 0, e
4. Find Bk (K).
30 Chapter 3. Homology

(a) When working in the highest dimension, note that Bk (K) = 0, e since
there are no (k+1)-chains for which the k-chains can form boundaries.
(b) Otherwise, look back to (2) in the next highest dimension, where you
already computed which k-chains are boundaries of (k + 1)-cells.
e then Hk (K) = Zk (K).
(c) Note that if Bk (K) = 0,
5. Compute Hk (K), by taking Zk (K) from (3) and using any homologies
found in (4).
Let’s go through a few examples.

Example 3.3.6. We have already worked with the sphere in Figure 3.2a, now
it is time to compute its homology groups. Call the 2-cell and give it a
clockwise orientation. There are no cells of higher dimension than 2, therefore
e for k > 2.
Hk (S2 ) = 0,
H2 (S2 ) :

1. There is only one 2-cell: , therefore C2 (S2 ) = h i ' Z.

2. @( ) = a a + b b = 0. This means that is a 2-cycle.
3. The 2-cycle generates the whole group of 2-cycles: Z2 (S2 ) = h i ' Z.
4. e
Because there are no 3-cells B2 (S2 ) = 0.
5. We get that H2 (S2 ) = Z2 (S2 ) ' Z.

H1 (S2 ) :
1. There are two 1-cells: a and b, therefore C1 (S2 ) = ha, bi ' Z Z.
2. @(a) = P Q 6= 0, @(b) = R Q 6= 0. Neither a nor b are 1-cycles. The
only 1-cycle is the trivial 0.
e
3. So Z1 (S2 ) = 0.
4. The only 1-chain that is a 1-boundary (bounds ) is 0 = a a + b b,
e
therefore B1 (S2 ) = 0.
5. We get that H1 (S2 ) = 0.e

H0 (S2 ) :

1. C0 (S2 ) = hP, Q, Ri ' Z3

2. @(P ) = @(Q) = @(R) = 0
3. Z0 (S2 ) = hP, Q, Ri ' Z3
4. From the calculations of H1 (S2 ), step 2, we have that P ⇠ Q ⇠ R because
@(a) = P Q 6= 0, @(b) = R Q 6= 0.
5. Combining Z0 (S2 ) with the homology relations (Q, R are in P̄ ) from step
4 gives H0 (S2 ) = hP̄ i ' Z.
3.3. Homology Groups 31

Example 3.3.7. Take the complex on the torus shown in Figure 3.2b. Call
the 2-cell and give it a clockwise orientation. There are no cells of higher
dimension than 2.

H2 (T2 ) :
1. There is only one 2-cell: , therefore C2 (T2 ) = h i ' Z.
2. @( ) = a + b a b = 0. This means that is a 2-cycle.
3. The 2-cycle generates the whole group of 2-cycles: Z2 (T2 ) = h i ' Z.
4. e
Because there are no 3-cells B2 (T2 ) = 0.
5. We get that H2 (T2 ) = Z2 (T2 ) ' Z.

H1 (T2 ) :
1. There are two 1-cells: a and b, therefore C1 (T2 ) = ha, bi ' Z Z = Z2 .
2. @(a) = @(b) = P P = 0. Both a and b, and any linear combination of
them, are 1-cycles.
3. The 1-cycles a and b generate the group of 1-cycles: Z1 (T2 ) = ha, bi ' Z2 .
4. The only 1-chain that is a 1-boundary (bounds ) is 0 = a + b a b,
e
therefore B1 (T2 ) = 0.
5. We get that H1 (T2 ) = Z1 (T2 ) ' Z2 .

H0 (T2 ) :
1. C0 (T2 ) = hP i ' Z
2. @(P ) = 0
3. Z0 (T2 ) = hP i ' Z
4. From the calculations of H1 (T2 ), step 2, we have that @(a) = @(b) =
P P = 0. Which gives us that B0 (T2 ) = 0. e
5. Thus H0 (T2 ) = Z0 (T2 ) ' Z.

Example 3.3.8. Take a look at the complex in Figure 3.6. Call this complex
K. Observe that forms a sphere and that there are no cells of dimension 3 or
higher.
H2 (K) :
1. and ⌧ are the only 2-cells and they generate the group of all 2-chains;
C2 (K) = h , ⌧ i ' Z2 .
2. @( ) = 0 and @(⌧ ) = f + g e, so is a 2-cycle.
3. The group of 2-cycles is Z2 (K) = h i ' Z.
e since we have no 3-cells.
4. B2 (K) = 0
32 Chapter 3. Homology

a d
v3 v7
b
e g
v1 v2
⌧
c v5 v6
v4 f
a

Figure 3.6: Complex K for Example 3.3.8.

5. H2 (K) = Z2 (K)/B2 (K) = Z2 (K) ' Z.

H1 (K) :
1. There are seven 1-cells; a, ..., g. These generate the C1 (K), so C1 (K) ' Z7 .
2. @(d) = @(f + g e) = 0, so d and f + g e (and any multiple of these)
are the only 1-cycles.
3. Z1 (K) = hd, f + g ei ' Z2
4. Homology relations
• From 2. we get that e ⇠ f + g. f + g e is a 1-boundary because it
is the boundary of a 2-chain i.e. ē is one of the generators of B1 (K).
• Looking at d we see that it is not the boundary of any 2-chain hence
d¯ is not a generator for B1 (K).
• B1 (K) = hēi ' Z.
5. This gives us H1 (K) = hdi ¯ ' Z.

H0 (K) :
1. C0 (K) = hv1 , ..., v7 i
2. @(vi ) = 0, i = {1, ..., 7}
3. Z0 (K) = hv1 , ..., v7 i ' Z7
4. From the calculations of H1 (K), step 2, we have that v1 ⇠ v2 ⇠ v3 ⇠ v4
and v5 ⇠ v6 ⇠ v7 , so there are only two equivalence classes v¯1 and v¯5 .
B0 (K) = hv1 v2 , v1 v3 , v1 v4 , v5 v6 , v5 v7
5. Combining Z0 (K) with the homology relations found in step 4 gives H0 (K) =
hv¯1 , v¯5 i ' Z2 .
Thees homology groups have given us the information that the complex has
two connected components, one cavity similar to a sphere, and another cavity
similar to a circle. The rest of the structure is disregarded, it does not add new
information. We regard all structures containing two components, one circle,
and one sphere, as the same.
3.3. Homology Groups 33

In summary, homology is a powerful tool for studying and differentiating

spaces. It helps us describe the structure of spaces in dimensions we cannot
visualize. It can for instance be applied in the study of structures in data sets.
Simplexes are cells with extra restriction. We could have chosen to work only
with simplexes, this would have yielded a homology called simplicial homology.
A powerful result is the fact that the homology groups obtained in simplicial
homology actually coincides with the homology groups we have obtained. This
is however not an easy feat to prove and the interested reader is refereed to [6]
for a detailed account.
We will end this chapter by building a bridge into knot theory. In knot
theory we will make use of something called polyhedral surfaces.
Definition 3.3.9. A polyhedral surface is a triangulable surface (or 2-manifold)
possibly with boundary.

If we can construct a surface (with or without) boundary from triangles or 2-

simplexes, following the rules of triangulation, we call this a polyhedral surface.
A cylinder is an easy example of a polyhedral surface. Viewing the cylinder
as a rectangle and imagine dividing the rectangle into two triangles gives a
triangulation of the cylinder. By having complexes on a surface we know that
there are tools that help us study these surfaces. In the chapter on knot theory
the boundary of a surface will be the most important part, as it is actually a
knot, and the techniques developed in this chapter will allow us to study the
knot using this surface, but more on that later.
Orientation has been mentioned earlier and the following definition agrees
with the one previously given but is stated only for polyhedral surfaces.

Definition 3.3.10. A polyhedral surface is orientable if it is possible to orient

each triangle in such a way that that when two triangles meet along an edge,
the two induced orientations run in opposite directions.
For polyhedral surfaces to be oriented we need that when two triangles are
glued together along an edge the induced orientations on the edge run in opposite
directions and therefore cancel out.
Definition 3.3.11. The Euler characteristic for a polyhedral surface S with
a triangulation consisting of F triangles, E edges and V vertices, is given by
(S) = F E + V .
The Euler characteristic is defined for simplexes but in fact we can use any
complex on a triangulable surface to calculate it if we let F be 2-cells, E be 1-
cells and V be 0-cells. This follows from the fact that homology and simplicial
homology are equivalent.
34 Chapter 3. Homology

Example 3.3.12. We have previously worked with the complexes in Figure

3.2, let us do so again. Both the sphere S2 and the torus T2 are triangulable
and orientable. From the complexes in the figure we have that

(S2 ) =1 2+3=2
2
(T ) =1 2+1=0

The reader can check that if a triangulation on the sphere is constructed, by

adding say a 1-cell connecting P and R, the Euler characteristic does not change.
Neither does adding a diagonal 1-cell in the complex on T2 .
We have now studied both homology groups and the Euler characteristic and
with the help of Betti numbers, see below, we will combine them. The Betti
numbers are topological invariants that aid us in our study of spaces.

Definition 3.3.13. The Betti numbers of a complex K are k = rk(Hk (K)).

Theorem 3.3.14 (cf. [2]). The Euler characteristic of a finite complex K is
given by the formula
Xn
(K) = ( 1)k k ,
k=0

where n is the dimension of K.

Definition 3.3.15. The genus of a connected orientable surface S is given by

2 (S) B
g(S) = ,
2
where B is the number of boundary components of the surface.
Example 3.3.16. Neither the sphere nor the torus have boundary and therefore
g(S2 ) = 0 and g(T2 ) = 1. The cylinder on the other hand has boundary, 2
boundary components to be exact, and can be triangulated with two triangles
giving it Euler characteristic 0 and genus 2 02 2 = 0.
Chapter 4

Knot Theory

In the introduction a knot was described as something that is formed when we

take a string, tie it, and then glue the ends of the string together. If you do not
attach the ends together the string can be tied and untied over and over again
in different ways. In this chapter a mathematical definition of a knot is given
and several knot invariants are defined, some more helpful than others. The last
two sections are dedicated to two knot polynomials: the bracket polynomial and
the Jones polynomial. Both are invariants and have contributed greatly to this
field.

4.1 Introduction to Knot Theory

In this secton we follow: [1] [3], [13] and [14]. In this work we study knots that
are embedded in S3 . One can project a knot onto a plane (or simply draw it
on a paper). These projections are called knot diagrams, see Figure 4.1. To
avoid ambiguity there are a few restrictions:

1. At each crossing it is clear which string segment passes over respectively

under the other (this is usually done by drawing a gap in the bottom
segment).
2. Each crossing involves exactly two segments of the string.
3. The segments must cross transversely.

Some intuitive terminology: At each crossing there is always one over-

strand and one understrand. An arc is a piece of the knot that passes from
one undercrossing to another with only overcrossings in between, i.e., an

Ahlquist, 2017. 35
36 Chapter 4. Knot Theory

Figure 4.1: Figure 8 knot.

Figure 4.2: Knot table - by Wikipedia user Jkasd [22], published with permis-
sion.

"unbroken" line in the diagram. We will work extensively with the knot dia-
grams but it is important to remember that these diagrams are only projections
of the knot.
Definition 4.1.1. K is a knot if there is an embedding h : S1 ! S3 whose
image is K. We say that K ✓ S3 is homeomorphic to the unit circle S1
The actual knot is a smooth embedding of the unit circle in S3 . The diagrams
are, in fact, sufficient for showing all results that are covered in this work. Why
this is true will be dealt with shortly. A knot can only consist of one component,
a link on the other hand is a finite union of disjoint knots. Many of the following
concepts can be generalized to links.
When studying knots one matter of great importance is being able to tell
knots apart (as well as being certain when they are one and the same). It will
later be apparent just how hard this actually is. For now you should know that
4.1. Introduction to Knot Theory 37

Figure 4.3: Wild knot - by Wikipedia user Jkasd [21], published with permission.

we are able to tell many knots apart, although, there exists no method that can
fully distinguish all knots from each other. Finding methods for differentiating
knots means finding knot invariants, that is, properties that remain unchanged
no matter which projection or embedding of the knot we happen to be studying.
We will work our way though several invariants all the way to the famous Jones
polynomial which was revolutionary when discovered. To do this we must first
specify what is meant by two knots being "the same".
Definition 4.1.2. Knots K1 and K2 in S3 are equivalent if there exist a home-
omorphism h : S3 ! S3 such that h(K1 ) = K2 .
We work with knots in the space S3 and we consider two knots to be two
representations of the same knot if there is a homeomorphism of the whole space
that takes one representation to the other. A tame knot is a knot that can
be constructed with line segments. This ensures that the knots are "nice" to
work with, e.g. shrinking a part of the knot to a point is not allowed, neither
are knots that need an infinite construction. A knot that is not tame is called
a wild knot, see Figure 4.3. All knots in this thesis are tame knots.
Definition 4.1.3. If H is an isotopy between ambient spaces, that is H :
S3 ⇥ I ! S3 , then H is an ambient isotopy.
Ambient isotopy is a stronger requirement than just the existence of a home-
omorphism between knot embeddings. By looking at knots from this perspective
we can utilize algebraic methods in our study and in fact no information is lost.
Even though structure is gained it would still be very tedious and hard work
to explicitly construct ambient isotopies between spaces whenever we wish to
show that two knots are equivalent. Thankfully this is not necessary. Work
done by Reidemeister integrated combinatorial techniques into knot theory and
these are very easy to work with. The following definition describes what is
called the Reidemeister moves. These operations work with the knot diagrams
rather than the actual knot. The pictures in the definition only show a small
part of the diagram, the rest remains unchanged.
38 Chapter 4. Knot Theory

Definition 4.1.4. The Reidemeister Moves.

R1: ⌦ ⌦

R2: ⌦ ⌦

R3: ⌦

So, what can we do with the Reidemeister moves? Well R1 allows us to

remove (or introduce) a twist in a diagram. The result is that the knot will
have one fewer (or one more) crossing. R2 lets us separate two strings that lie
on top of each other or vice versa. This will add or remove two crossings. R3
allows us to move a strand from one side of a crossing to the other. This also
works if the strand being moved is above the other two strands. R3 does not
affect the number of crossings in the current projection. If a deformation of
the diagram only uses R2 and R3 we call this a Regular isotopy (or planar
isotopy). A word of caution: regular isotopy is an equivalence relation for the
knot diagrams and is not defined for the knot embedding.
The Reidemeister moves only describe procedures performed on the dia-
grams. It is not intuitively clear that studying knot diagrams is a technique
strong enough to allow us to draw conclusions about the actual knot. Fortu-
nately it is a very strong technique, which is shown in the following theorem.

Theorem 4.1.5 (Reidemeister’s theorem). If two knots K1 and K2 are ambient

isotopic, then there is a sequence of Reidemeister moves taking a projection of
K1 to a projection of K2 .

Proof by Kauffman in article [10]. Reidemeister not only defined these moves
for knot diagrams he proved that one can, using only R1-R3, always transform
two knot projections into one another if and only if they are projections of the
same knot.

Example 4.1.6. The knot in Figure 4.4 is equivalent to the unknot. Use the
Reidemeister Moves to convince yourself of this.

We are striving to find ways to tell knots apart. It feels intuitively obvious
that there exists more knots than just the unknot and with the next result we
can show that there exists (at least) two different knots. Another name for the
4.1. Introduction to Knot Theory 39

Figure 4.4: Unknot in disguise.

unknot is the trivial knot, and all knots distinguishable from the unknot are
therefore called non-trivial knots.

Definition 4.1.7. A knot diagram is tricolorable if each arc in the knot digram
can be assigned a single color such that

1. at least two colors are used, and

2. at each crossing all three incident arcs are either all different colors or the
same color.

Figure 4.5: Tricoloring of trefoil.

In Figure 4.5 it is shown that the this projection of trefoil knot is tricolorable.

Theorem 4.1.8 (cf. [14]). If a diagram of a knot, K, is tricolorable, then every

diagram of K is tricolorable.

Proof. (Outline) By tricoloring the Reidemeister Moves one can see that they
do not affect the color of the rest of the diagram. This means that they cannot
alter tricolorability for a knot diagram, and hence, if one diagram is tricolorable
all are.
40 Chapter 4. Knot Theory

This makes tricoloring a knot invariant. The unknot is not tricolorable, thus
it is different from the trefoil. In the knot table, Figure 4.2, only knots 31 , 61 ,
74 and 77 can be colored. Observe that we cannot yet distinguish the colorable
(or uncolorable) knots from each other, at the moment we can only be certain
that there exists two different knots - the trivial and a non-trivial.
The knots in the knot table, Figure 4.2, are labeled in the Alexander-Briggs
notation. This organizes knots based on their crossing number, the subscript is
just a counter to separate knots with the same crossing number.
Definition 4.1.9. The crossing number, c(K) of a knot K, is the minimum
number of crossings that occur in any diagram of K.
Example 4.1.10. For the unknot we have that c(unknot) = 0. The projections
of the trefoil seen so far all have 3 crossings, so is c(tref oil) = 3? Yes, it is.
Simply because there are no knots such that c(K) = 1 or 2. To show this first
draw one crossing and connect the ends in all 4 possible ways: this only yields
the unknot. Then draw two crossings and connect the ends in all possible ways:
this gives the unknot, two unknots (which is a link), the Hopf link. Therefore 3
is the minimum number of crossings you need to draw the trefoil. The crossing
number is not easy to find, you need to prove there are no representations of the
knot with fewer crossings, and right now we cannot show that knot 62 is in fact
not just a more complex diagram of any of the knots with fewer crossings. We
will find a way to do so later. The crossing number for a knot is an invariant,
but at the moment not a very helpful one.
Definition 4.1.11. A knot is oriented if it has an orientation assigned to it.
This is illustrated by arrows.
Orientation is extra information that can be added to the knot diagram. If a
knot K has a given orientation we take K to mean K with reverse orientation.
A knot is called invertible if K and K are equivalent. All knots in Figure
4.2 are invertible. The first non-invertible knot is one with eight crossings (817 )
[20].

(a) +1 crossing. (b) 1 crossing.

Figure 4.6: Positive and negative crossing.

Definition 4.1.12. The writhe of an oriented knot, w(K), is the sum of the
crossings with signs as shown in Figure 4.6.
4.2. Prime Decomposition Theorem 41

Example 4.1.13. The writhe of the trefoil in Figure 4.5 is 3 regardless of

given orientation.
The writhe is a regular isotopy. It is not an invariant under R1, only for R2
and R3.
Definition 4.1.14. A knot K is called alternating if it has a diagram in which
undercrossings and overcrossings alternate around K.
All knots with crossing number 7 or less are alternating. For knots with eight
crossings there exists only three unaltering knots [19]. The first unalternating
knot is 819 .
Definition 4.1.15. The knot sum or connected sum K1 #K2 , is formed by
placing two knots side by side, removing a small arc from each knot and then
joining the knots together with two new arcs.
A knot is called composite if it can be written as the sum of K1 and K2 ,
neither of which is the unknot and prime if it is not composite. Knot tables
only show prime knots, see Figure 4.2.
Example 4.1.16. K#(unknot) = K, 8 knots K.

4.2 Prime Decomposition Theorem

For this next part we will develop the theory for prime decomposition. We have
already defined what a prime knot is, but similarly to positive integers all knots
have a unique factorization into prime knots. A knot is either prime or it can be
decomposed into at least two non-trivial knots. If these factors are not prime we
can continue. This will give a unique decomposition. This chapter will utilize
results such as polyhedral surfaces, Euler characteristic and genus as defined in
previous chapters.
Definition 4.2.1. An orientable surface with a knot as its boundary is called
a Seifert surface for the knot.
Theorem 4.2.2 (cf. [14]). Every knot is the boundary of an orientable surface.
This was proven by Seifert in the 1930’s. The proof relies of a construction
now refereed to as the Seifert algorithm which produces a Seifert surface for a
given knot projection.
The Seifert Algorithm
1. Fix an orientation for a projection of the knot.
42 Chapter 4. Knot Theory

2. Let x be a point on an arc, arbitrarily chosen.

3. Begin at x and travel in the direction of the arc. Whenever you reach a
crossing change strands and follow the new strand in its direction. Do this
until you end up back at x.
4. If there is an untraced part of the diagram, chose a new point x and
start again. Repeat this until you have traveled along the entire diagram.
The result is a collection of circles (Seifert circles) each of which is the
boundary of a disk in the plane. If circles are nested "lift" the inner ones
to a plane above, so you wary the heights of the different the disks.
5. Connect the disks by attaching bands at the points corresponding to the
crossings in the original diagram. When attaching a band add a half-twist
to it. The twist should reflect the crossing it represents, that is, it should
follow the rotation of that crossing.
This construction yields an orientable surface with the knot as its boundary.
A knot can have different Seifert surfaces, it depends on the knot projection one
starts with.
Example 4.2.3. By following the Seifert algorithm for the star knot (51 ) one
first gets two Seifert circles (on top of each other). After attaching twisted bands
at all five crossing points (that match the orientation of the original crossings)
one gets a surface that looks like the one in Figure 4.7.

Figure 4.7: Seifert surface for 51 .

Example 4.2.4. The trefoil knot has a surface quite similar to the star knot.
It has two disks above each other, but with five connecting bands instead of
three. All bands twist in the same direction.
4.3. Bracket Polynomial 43

Definition 4.2.5. The genus of a knot, g(K) is the minimum possible genus of
a Seifert surface for the knot.
For the minimal projection of the unknot the disk is its Seifert surface whose
genus is zero. In fact, if g(K) = 0 for a knot K, then K is the unknot [13].
From the construction of the Seifert surfaces one gets the following relation:
If the knot diagram had n crossings and s Seifert circles were obtained then
g(K)  12 (n s + 1). One of the most useful results about knot genus is its
additivity.
Theorem 4.2.6 (cf. [13]). For any two knots K1 and K2 , g(K1 #K2 ) = g(K1 )+
g(K2 ).
Theorem 4.2.7 (cf. [14]). Every knot can be decomposed as the connected sum
of non-trivial prime knots. If K = K1 #...#Kn , and K = J1 #...#Jm , with each
Ki and Ji non-trivial prime knots, then m = n and, after reordering, each Ki
is equivalent to Ji .
Theorem 4.2.8 (cf. [14]). If K is nontrivial, there does not exist a knot J
such that K#J is trivial.
This is analogous to the fact that multiplying two positive integers can never
yield 1.

4.3 Bracket Polynomial

This section is devoted to the bracket polynomial, also known as the Kauffman
bracket after Louis Kauffman. Two of Kauffman’s articles, [8] and [9], are the
basis for this section and the next.
Definition 4.3.1. The Bracket polynomial Let K be an unoriented knot or link
diagram. Let hKi be the element of the ring Z[A, B, d] defined by means of the
rules:
D E
=1 (4.1)
D E D E
[ K = d K , K not empty (4.2)
D E D E D E
=A +B (4.3)

The last equation shows only parts of the diagram, and as with the Rei-
demeister moves knot and link diagrams may only differ in this one indicated
crossing. A rule to help you remember: one gets A when turning right on the
underpass (and similarly B when turning left).
We will start with an example - the bracket of the Hopf link.
44 Chapter 4. Knot Theory

* +
=

* + * +
A +B =

* + * + * + * +
2 2
A + AB +BA +B =

A2 d + 2AB + B 2 d

Figure 4.8: Bracket polynomial for the Hopf link.

Example 4.3.2. Look at Figure 4.8. Starting with the Hopf link, we split the
crossing marked with the dashed circle. This gives two outcomes according to
rule 3 in the definition. Since there are still crossings left we continue the process
and choose one new crossing in each of the diagrams and split again. The result
is 4 diagrams with a total of 6 unknots. Using rules 1 and 2 from the definition
we can complete the bracket polynomial.

Our goal is to investigate if the bracket polynomial is an invariant. To do

this we must check it against the Reidemeister moves. As shown below, we start
with one of the diagrams associated with R2 and examine how it is affected by
the bracket polynomial.
4.3. Bracket Polynomial 45

Satisfying the Reidemeister moves, starting with R2:

⌧ ⌧ ⌧
=A +B
⌧ ⌧ ⌧ ⌧
= A2 + AB + AB + B2
⌧ ⌧ ⌧ ⌧
= A2 + ABd + AB + B2
⌧ ⌧
= (A2 + B 2 + ABd) + AB
⌧
?
=

⌧ ⌧
R2 says that = , therefore we must have AB = 1, which
gives that B = A 1 , and A2 + B 2 + ABd = 0, which gives that d = A2 A 2 .
By accepting these restrictions on the variables we make sure that R2 does not
change the polynomial. By using R2 we can now look at R3.

⌧ ⌧ ⌧
=A +B
⌧ ⌧ ⌧
=A +B = AB

Remark. Between the first and second line we use R2.

By choosing B = A 1 and d = A2 A 2 we have now made sure that the

polynomial is unchanged by the Reidemeister moves R2 and R3. What a great
result! This means that the bracket polynomial for the Hopf link in Figure 4.8
becomes A4 A 4 .
Remembering the earlier definitions of regular and ambient isotopy, we have
now shown that the bracket is at least an regular isotopy invariant. Is it also an
ambient isotopy? Ambient is always the goal, since it is a far stronger invariant
than regular. For the calculations on R1 both crossing directions must be looked
at, this gives that
46 Chapter 4. Knot Theory

⌧ ⌧ ⌧
1
=A +A
⌧ ⌧
1 2 2
=A +A ( A A )
⌧
3
= A ,

and, with almost identical calculations, that

⌧ ⌧
= A3 .

Here we run into trouble. While R2 and R3 left the polynomial unchanged,
we can clearly see that this is not true for R1. The bracket polynomial preserves
regular isotopy (but not ambient). Moving the knot around like a ribbon flat
on a table is permitted but lifting it from the surface to induce a twist is not.
This is still a good result, we are able to study knots based on their respective
polynomial but we did want an invariant that can handle all of the Reidemeister
moves, i.e., we want ambient isotopy.
Remark. For the interested reader: In [9] Kauffman studies two invariants of
regular isotopy. It is outside the scope of this paper but a very interesting read!
Example 4.3.3. The backet polynomial for trefoil in Figure 4.5 is hKi =
A 7 A 5 A3 . When splitting the first crossing one of the new knots it
the Hopf link previously calculated. By following the procedure for the other
knot one gets the stated polynomial.

4.4 Jones Polynomial

The bracket polynomial hKi 2 Z[A, A 1 ] is a Laurent polynomial in A. To
obtain an ambient invariant from this, we will use the writhe of the knot in
order to "fix" the trouble that R1 caused. Recall that the writhe is the sum of
the signs of crossings. The move R1 has the following effect.

✓ ◆ ✓ ◆
w =1+w
✓ ◆ ✓ ◆
w = 1+w
.
4.4. Jones Polynomial 47

Definition 4.4.1. Let F (K) 2 Z[A, A 1

], a Laurent polynomial, and define
3 w(K)
F (K) = ( A ) hKi.

Theorem 4.4.2 (Kauffman, [8]). F (K) is an ambient isotopy invariant.

Proof. hKi and w(K) does not change under R2 and R3 () regular isotopy.
R1 changes the bracket by the factor A±3 , w(K) is meant to nullify this.

✓ ◆ ⌧
3 w
F = A
⌧
3 w
= A

So we get that ✓ ◆ ✓ ◆ ✓ ◆
F =F =F ,

and this concludes the proof.

The writhe can in fact be used to normalize any regular isotopy to obtain
an ambient isotopy.

(a) L+ (b) L (c) L0

Figure 4.9: Crossings for the skein relation

Definition 4.4.3. The Jones polynomial, VK (t), for a knot or link is a Laurent
polynomial in t1/2 satisfying the following properties:

1. For an oriented knot or link K, VK (t) 2 Z[t, t 1 ] is an ambient isotopy

invariant of K.
2. Vunknot = 1.
3. The skein relation: t 1 VL+ tVL = (t1/2 t 1/2 )VL0 .

Jones first published this polynomial in [7]

Theorem 4.4.4 (Kauffman, [8]). VK (t) = F (K) for A = t 1/4

.
48 Chapter 4. Knot Theory

Proof. Vunknot (t) = 1 = F (unknot), property 2. from the definition holds.

D E D E D E
hL+ i = =A +A 1
D E D E D E
hL i = =A +A 1 , which gives
D E D E D E
A A 1 = (A2 A 2 ) .

Adjusting the formula with the writhe of each diagram we get

A4 F (L+ ) A 4
F (L ) = (A 2
A2 )F (L0 ),

and substituting A = t 1/4 , gives the skein relationship in the definition and
since F (K) is ambient so is VK (t), which completes the proof.
With the bracket polynomial Kauffman constructed another (easier) way to
prove that the Jones polynomial is an ambient isotopy invariant.
Example 4.4.5. With this polynomial we can tell several different knots apart.
All knots in the in Figure 4.2 have different polynomials. To give a few examples:
• The figure 8 knot in Figure 4.1 has polynomial VK (t) = t2 t+1 t 1 +t 2

• The star knot, 51 , has the polynomial VK (t) = t2 + t4 t5 + t6 t7

• The 62 knot has the polynomial VK (t) = t 1 + 2t 1 2t 2 + 2t 3
2t 4 + t 5 p
• The Hopf link Figure 4.8 has the polynomial VK (t) = t(1 + t2 )
Chapter 5

Tangles and DNA

This chapter starts with an introduction to the theory of tangles. A tangle is a

part of a knot (or link) and one only works with this part, rather than with the
whole knot. Figure 5.1a depicts a tangle diagram, envision the knot continuing
outside the circle. After the section on tangle theory we move on to DNA and
apply what we have learned to the study of enzyme and DNA interaction. More
specifically we target the recombination enzyme called resolvase.

5.1 Tangles
This section relies on the literature [1] and [15] as well as the article [4]. The
closed 3-ball B 3 is bounded by the sphere S2 . Fix two points on the sphere (say
the north and south pole) and attach a curve between them embedded in B 3 .
The curve can be knotted but self-intersections are not permitted. This is called
a (1, 1)-tangle. Similarly, fixing 4 points on the sphere (preferably evenly spreed
on a great circle) and connecting them with two curves embedded in B 3 gives
(2, 2)-tangle. So, 2n fixed points connected by n curves is called a (n, n)-tangle.
A tangle is the set (B 3 , T ), where T is the collection of curves joining the points
in pairs. This notation will be shortened and we let T denote the tangle.
There are several different type of tangles but all tangles henceforth will be
(2, 2)-tangles, and for simplicity refereed to as tangles. Some terminology for
the fixed points on S2 : denote these NW, NE, SW and SE (for north west,
e.t.c.). A tangle diagram is a projection formed according to the rules of knot
diagrams with the extra restrictions the points {NW, NE, SW, SE} should end
up as shown in Figure 5.1.
If you connect NW with NE, and SW with SE, outside of B 3 , as shown in

Ahlquist, 2017. 49
50 Chapter 5. Tangles and DNA

(a) (b)

Figure 5.1: Two examples of tangles.

Figure 5.2, you have formed the numerator of T, denoted N (T ). Connecting

NW with SW, and NE with SE instead, give the denominator of T, D(T ). The
numerator and the denominator gives us a natural connection between knots (or
links) and tangles. This make it possible to view a tangle as a part of a knot,
so many concepts for knots can be extended to tangles.

T
T

(a) N (T ) (b) D(T )

Figure 5.2: Numerator and denominator of a tangle.

Definition 5.1.1. If an orientation-preserving homeomorphism f : B 3 ! B 3

satisfies the following conditions, then the tangles T1 and T2 are said to be
equivalent:

1. f is the identity map for S2 , i.e., the map keeps S2 fixed,

2. f (T1 ) = T2 .

As for knots, Reidemeister moves can be used to manipulate the tangle

diagrams. It is, however, important to remember that the strings can never be
5.1. Tangles 51

(a) T1 (b) T2 (c) T1 + T2

Figure 5.3: Tangle sum

(a) (0)-type (b) (0,0)-type (c) (-1)-type (d) (1)-type

Figure 5.4: Exceptional tangles

drawn outside the circle. This would represent a part of the tangle leaving B 3
and in doing so creating more intersections in S2 .
The formal sum of tangles, T1 +T2 be formed by gluing the east hemisphere
of B13 (containing T1 ) to the west hemisphere of B23 (containing T2 ) identifying
NE and SE of T1 to NW and SW of T2 respectively. Lastly remove the gluing
face to make one ball B 3 containing T1 +T2 . This is illustrated diagrammatically
in Figure 5.3. A vital observation is that even if N (T1 ) and N (T2 ) are non-trivial
knots N (T1 + T2 ) could still yield the unknot (or a trivial link).
Look at the tangles shown in Figure 5.4. These are four different types of
tangles, the (0)-type, (0,0)-type also called the (1)-type,(-1)-type and (1)-type
respectively. Collectively we call these tangles the exceptional tangles. With
knots we restricted ourselfs to tame knots, similarly we shall now restrict our
study to what is called rational tangles.
Definition 5.1.2. Suppose f is a homeomorphism that maps the ball B 3 to
itself and maps the set of points {NW, NE, SW, SE} to itself, but not necessarily
as the identity map (i.e. f need not map NW to NW e.t.c.). A rational tangle is
a tangle that is the image of the (0, 0)-type tangle under this homeomorphism.
Rational tangles are in some literature refereed to as trivial tangles. All
exceptional tangles are rational, by rotating (0, 0) by ⇡2 we can obtain (0).
Imagine holding the ball with (0, 0) in it, induce a half twist by taking the
points SW and SE and rotating them around each other so they change places,
this will give you either ( 1) or (1) depending on which direction you rotate.
There are many rational tangles and one way to form them is by doing twists,
just as the one just described. A vertical twist is a twist around a vertical
52 Chapter 5. Tangles and DNA

(a) V +2 (b) V -2 (c) H +2 (d) H -2

Figure 5.5: Orientations of vertical and horizontal twists

axis that keeps NW and NE fixed but interchanges SW and SE. A horizontal
twist it a twist around a horizontal axis performed by keeping NW and SW
fixed and rotating so that NE and SE interchange. Each twist has a natural
orientation, we call them positive twists and negative twists (denoted by
+ and - respectively), see Figure 5.5. Look at the exceptional tangles: ( 1) is
obtained either by a negative vertical twist of (0) or a negative horizontal twist.
Similarly the (1)-type comes from positive twist.
Description of vertical and horizontal twists. All trivial tangles can be
made from (0) or (0,0) using only vertical and horizontal twists.
If we alternate between horizontal and vertical twists we get more complex
looking tangles. A tangle constructed from twists will be denoted T (a1 ...an )
where (a1 ...an ) describes the sequence of twists in the following way:

• If n even, start with the (0, 0)-type, make a1 vertical twists followed by
a2 horizontal, and so on alternating the twists, until you finally perform
an horizontal twists.

• If n odd, start with the (0)-type, make a1 horizontal, a2 vertical,..., an

horizontal.

We allow ai = 0, so we can have T (3, 0) for example. It is beneficial, or

rather it will give us a shorter notation, if we require that ai 6= 0, for i 6= n.
The following example illustrates why this restriction works.

Example 5.1.3. The tangles is Figure 5.1 are Ta ( 2, 1, 1, 0) and Tb (2, 2, 3).

Example 5.1.4. The tangle T (1, 5, 0, 2) can also be described as T (1, 3). The
five positive twists and the two negative twist end up next to each other (since
a3 = 0) and by the Reidemeister move R2 this is equivalent to just 3 positive
twists.

Rational tangles can if fact be completely determined by the sequence of

alternating twists [15]. The knots and link obtained by the denominator of a
5.2. DNA 53

rational tangle are actually a special kind of family of knots and links called
4-plats (also known as rational or 2-bridge knots and links). The set of 4-plats
has been completely classified [15].

5.2 DNA
This section relies on extraordinary work done by C. Ernst and D. W. Sumners,
[4] and [17]. DNA (deoxyribonucleic acid) is our genetic code. DNA is made
form alternating sugar and phosphors and most of our DNA is organized on two
strands (backbones) that twist around each other in a double helix. For the
purpose of this work the double helix will be seen as one string in 3-dimensional
space.
The genome is involved in several actions, there are for example, enzymes
that perform transcription, replication, and, recombination of the DNA. We
view an enzyme as a ball B 3 and call this the enzyme ball. It is not possible
for us to observe the actions taking place inside the enzymes, so in order to
understand the action of an enzyme we must study the result (or product) of the
action. In this work we will focus on the actions of the enzyme recombinase.
Recombinase is a vital enzyme that moves segments or inserts new ones into the
genome.
The topological approach to enzymology uses mathematical tools to study
the geometrical (supercoiling) and topological (knotting and linking) properties
of DNA. This is an experimental protocol where one tries to determine the
enzyme mechanisms by combining laboratory experiments and topology. To
do this one produces large quantities of circular DNA that can be genetically
engineered to contain sites that the enzyme will react to. A solution with the
enzyme is added and gel electrophoresis is used to determine the products. With
the circular DNA as a starting point mathematical models can be made to study
what actions the enzyme performed.
When recombinase acts on the genome it bounds two strand of juxtaposed
DNA that both have sites recognized by the enzyme. These sites can be on
two different DNA molecules or on the same one. The bounded DNA together
with the enzyme is called synaptosome. The enzyme together with the DNA
strand(s) (both inside and outside the enzyme ball) is called the synaptic com-
plex.
We can model the actions of recombinase using mathematics, more specifi-
cally tangle theory will be used. Before beginning some biological assumptions
must be made that we can build our mathematical model on.
Assumption 5.2.1 (cf. [17]). The enzyme mechanism in a single recombina-
tion event is constant, independent of the geometry (supercoiling) and topology
54 Chapter 5. Tangles and DNA

(knotting and linking) of the substrate population. Moreover, recombination

takes place entirely within the domain of the enzyme ball, and the substrate
configuration outside the enzyme ball remains fixed while the strands are being
broken and recombined inside and on the boundary of the enzyme.
Assumption 5.2.2 (cf. [17]). The synaptosome is a (2,2)-tangle and can be
mathematically subdivided into the sum Ob + P of two tangles.
The tangle P in the assumption is called the parental tangle. It contains
the sites where the breakage and reunion of the strands occur. The outside
bound tangle Ob , is the part of the DNA strand bound by recombinase but not
affected by the recombination. The recombination event is modeled as follows:
we remove the tangle P and replace it by the recombinant tangle R. This
gives

pre-recombination synaptosome = Ob + P , and

post-recombination synaptosome = Ob + R.

Assumption 5.2.3 (cf. [17]). The entire synaptic complex is obtained from the
tangle sum (Of + synaptosome) by the tangle closure construction (the nomina-
tor).
From these assumptions we have four variables: R, P, Ob , and Of . The
assumptions give us two equations in these four variables:

N (Of + Ob + P ) = substrate, and

N (Of + Ob + R) = product.

Assumption 5.2.4 (cf. [17]). In processive recombination, each round of re-

combination adds a copy of the recombinant tangle R to the synaptosome.
If the enzyme, during a single bounding encounter, makes n recombinations
we will obtain a system of equations that instead look like this:

N (Of + Ob + P ) = substrate, and

N (Of + Ob + iR) = product, for i = 1, ..., n.

There are still only four variables but by each new recombination a new
equation is obtained. There are several different enzymes in the group recom-
binase and they will, naturally, have slightly different functions. So, with these
assumptions and tangle theory as a basis, it is time to look more closely at one
of the recombination enzyme: Tn3 resolvase. Using an electron microscope one
can take pictures of the synaptic complex formed when resolvase interacts with
5.3. Summary 55

a DNA loop. From the obtained results it is clear that the DNA strands outside
the synaptosome are untangled, thus Of = (0). This reduces our variables down
to three: R, P , and Ob .
From experiment conducted on the products generated by resolvase one has
found four different knots and links: the unknot, the Hopf link, the figure 8 knot,
and the Whitehead link. Relying on the assumptions, a fair amount of tangle
theory, and the experimental findings, the following theorem can be proved.
Theorem 5.2.5 (cf. [17]). Suppose that the tangles R, P , and Ob , satisfy the
following equations:
1. N (Ob + P ) = the unknot,
2. N (Ob + R) = the Hopf link,
3. N (Ob + 2R) = the figure 8 knot, and
4. N (Ob + 3R) = the Whitehead link.

Then Ob = T ( 3, 0), R = T (1) and N (Ob + 4R) = N (T (4, 3)) or the knot 62 .
The proof of this theorem relies on tangle theory that is outside the scope
of this work but the the reader is refereed to the joint work of C. Ernst and D.
W. Sumners [4] for a rigorous mathematical explanation of tangles and DNA
recombination.

5.3 Summary
This thesis started with some thorough background in topology and the main
concept was homeomorphic spaces. Homeomorphisms were then used several
times throughout this work, for instance in the definition of a knot. In Chapter
3 we looked at the construction of homology theory by defining concepts such
as cells and complexes. Thanks to homology we gained ways of understanding
the structure of a space. After homology we moved into the field of knot theory
where several invariants were described, the most prominent one was the Jones
polynomial. Finally, in this last chapter, knot theory (or rather tangle theory)
was used to shed light on how an enzyme acts on DNA.
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