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Roland Van Der Veen - Knots, Continued Fractions and DNA

The document summarizes a mathematics seminar about knots, continued fractions, and their application to DNA. It discusses the history of knot theory and introduces rational tangles and knots. Rational tangles can be represented by their own continued fractions. This allows knots to be classified and compared based on their continued fractions. The talk applies this to analyze experiments where an enzyme modifies a DNA loop, allowing determination of the enzyme's activity without knowing initial conditions.

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110 views14 pages

Roland Van Der Veen - Knots, Continued Fractions and DNA

The document summarizes a mathematics seminar about knots, continued fractions, and their application to DNA. It discusses the history of knot theory and introduces rational tangles and knots. Rational tangles can be represented by their own continued fractions. This allows knots to be classified and compared based on their continued fractions. The talk applies this to analyze experiments where an enzyme modifies a DNA loop, allowing determination of the enzyme's activity without knowing initial conditions.

Uploaded by

Lokosoo
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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AiO Seminar Mathematics: Friday 17-11, 16:00-17:00, Room P.

014

Knots, Continued Fractions and DNA

Roland van der Veen

A knot is a circle embedded in space


History of knot theory Rational tangles and continued fractions Classification of rational tangles and rational knots

Application to DNA

Peter Tait (1883)

Method: alternating knot diagrams


Tait Flyping Theorem (proven in 1990): Two alternating diagrams give rise to the same knot iff they are related by a sequence of flypes. Flype move:

T T

John Conway (1970)


Tangles

T
0

Rational tangles: Start with 0 and twist an odd number of times: right, down, right, down, right, Start with , and twist an even number of times: down, right, down, right,

Conways Classification Theorem


Let S and T be two rational tangles with twist sequences s1,, sm and t1,, tn. S and T are equal iff [sm ,, s1] = [tn ,, t1] [a ,b,c,d,e,f] is the continued fraction:

Proof, Louis Kauffman (2003)


Imitate the arithmetic of continued fractions with tangles:
3 -2 3 + -2 = 1

-T is T with all crossings reversed

1
T

= -

1 2

A rational tangle can be written as its own continued fraction!


continued fraction: [3,2] = 3 + 1 2 2,3

3 + 1 = 2

=
2,3

Every continued fraction has a unique canonical form: a positive/negative continued fraction of odd length.

Tangles with equal fractions are equal: Bring the tangles into canonical form. The corresponding fractions are also in canonical form. The canonical form is unique for fractions, so the fractions are equal.

Conversely: Tangles with different fractions are different.


Bring the fractions into canonical continued fraction form. Bring the tangles into canonical form. The forms look the same! The corresponding diagrams are alternating, so they are related by flypes (Tait flyping theorem). Flypes do not change the fraction. The fractions are assumed to be different, so the tangles are not the same.

Rational knots
A rational knot is the closure of a rational tangle. Notation: cl(T) =

cl(3) =

Theorem: cl(p/q) and cl(p/q) are equal iff 1. p = p 2. q = q (mod p) or qq = 1 (mod p)

Application to DNA

1.The DNA loop is twisted n times. 2.The enzyme X replaces the tangle 0 by r. 3.The result is the knot cl(10/7). 4.Determine r without knowing n.

Enzyme X
cl(1/n + r) the result is cl(10/7) nr + 1 = 10 and either n = 7 (mod 10) or 7n = 1 (mod 10) nr = 9, so n = 1, 3, 9. The possibilities are n = 3 Enzyme X acts by replacing the 0 tangle by 3

The infinite golden braid

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