Helen Farrell Supervisor: Dirk Schuetz

K NOTS
Reidemeister Moves
To deform a tangle without cutting the string, we can use the Reidemeister moves. Each move changes the projection of the knot, but it does not change the knot represented by the projection.

Introduction
Mathematically we think of a knot as a single closed curve in Euclidean 3-space that does not intersect itself, but we nd knots in everyday life. For a knot on a piece of string, it is possible to move the knot closer and closer to the end of the string until it falls off. To study knots, the knot must stay on the string, or it would be possible to transform any knot into an unknotted piece of string. To prevent this from happening, we can either have an innitely long string which contains no other knots, or we can join the ends of the string together to form a loop. We often nd the second option more practical. We will think of the string as having no thickness.

Joining Tangles
We have two methods to join one tangle to another, multiplication() and addition(+). For multiplication, place the tangles one above the other and join the SE and SW end-points of the upper tangle to the NE and NW end-points of the lower tangle respectively. For addition, place the tangles side by side and join the NE and SE end-points of the left hand tangle to the NW and SW end-points of the right hand tangle respectively.

DNA
Reidemeister moves are knot invariants, so we can use Reidemeister moves to show that two projections are the same knot.

Knot Theory
One of the most important questions in Knot Theory is Are these two knots the same (equivalent)?

Tangles
A rational tangle is the result of consecutive twists on neighbouring end-points of two trivial ones. The trivial tangles, [0] and [], and two other 2-tangles are shown below.

DNA is normally found as a long double stranded helix made up of two strands oriented in opposite directions, so that the overall DNA molecule is not oriented. DNA can also be found in a single strand, and as circular DNA. The most useful method to people looking at the effect of enzymes on a strand of DNA is to look at single stranded, circular DNA. This way, if the enzyme produces a result, we are able to see it, rather than have it slip off the end of the strand.

The number denotes the number of crossings in a knot, the subscript differentiates between knots with the same number of crossings. The most basic knot possible is the unknot, 01 , a simple loop.

Enzymes
A topoisomerase is a type of enzyme which breaks DNA strands, rearranges them, and then recombines the DNA. Let S denote the substrate tangle, and R the recombination tangle. Iterating the use of the topoisomerase allows us to work out what is does, by looking the products created. An example is Tn3 resolvase: N (S + T ) = K1 (the unknot) N (S + R) = K2 (the Hopf link) N (S + R + R) = K3 (the gure-eight knot) N (S + R + R + R) = K4 (the Whitehead link) From these equations, De Witt Sumners and Claus Ernst proved that S= [1] and R=[1]. 3

We can show that any knot is isotopic to the unknot using Bachelors Unknotting. To show that two knots are equivalent, we must show that they are ambient isotopic. Ambient isotopy is an equivalence relation on knots, two knots are ambient isotopic if one knot can be continuously deformed through 3-space into the other. The difference between an isotopy, and an ambient isotopy is that an ambient isotopy takes heed of the points around the knot, and requires them to move continuously along with the knot.

We label the end-points of the arcs NW, NE, SW, SE corresponding to the compass directions. If we take the closure of a tangle, we obtain a knot or a link. Rational knots are obtained by taking the numerator closure of a rational tangle. To take the numerator closure, N(T), we simply join the NW end-point to the NE end-point, and the SW end-point to the SE end-point.

Bachelors Unknotting
Imagine a knot on a string. We can make the knot smaller and smaller until it becomes a point on the string. Since the string does not have a thickness, the knot disappears. This is Bachelors unknotting.

Tangle Fractions
Tangles made by n horizontal twists are denoted [n], 1 while tangles made by n vertical twists are denoted [n] . The denominator closure, D(T), is obtained by joining NE to SE, and NW to SW. We obtain D(T) from N(T) by a [0] - [] interchange. This is similar in method to recombination in DNA, which makes tangles a good model for this.

References
Adams, Colin C., (2004) The Knot Book, American Mathematical Society Kauffman, L. H. and Lambropoulou, S., (2003) From Tangle Fractions to DNA, arXiv:math/0311511v1 Left hand column pictures from: http://www.oglethorpe.edu/faculty/j nardo/knots/intro.htm, and Burde, Gerhard and Zieschang, Heiner, (2002) Knots, Walter de Gruyter Co.