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A Majorcan Algebrist in King RNA's Court
A Majorcan Algebrist in King RNA's Court
A Majorcan Algebrist in King RNA's Court
Francesc Rosselló
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Contact structures of biopolymers
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Prediction, study and comparison of 3-dimen-
sional structures, central topics in computa-
tional biology.
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Contact structures of biopolymers
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RNA secondary structure
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RNA secondary structure. . . with
pseudoknots
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RNA tertiary structure
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Protein contact structure
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Let the algebra enter
[n] := {1, . . . , n}
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Edit distances for contact structures with
unique bonds
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Topological indices on RN An
v
u n
uX
p p
dmount(Γ1, Γ2) = t |fΓ1 (k) − fΓ2 (k)|p
k=1
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Involution representation and distance
Reidys-Stadler, 1996
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Given Γ1 = ([n], Q1), Γ2 = ([n], Q2) ∈ Un, their
symmetric difference is
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• Open orbit of Γ1∆Γ2: all other orbits; they
have exactly 2 nodes of degree 1.
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Subgroup representation and distance
Reidys-Stadler, 1996
Given Γ = ([n], Q) ∈ Un
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Matrix representation and distance
Magarshak 1993, Reidys-Stadler 1996
Given Γ = ([n], Q) ∈ Un
s1,1 . . . s1,n
SΓ = ... ... ...
∈ GL(n, Q),
sn,1 . . . sn,n
where
−1
if i 6= j and i · j ∈ Q
si,j = 1 if i = j and i · l ∈/ Q for every l
0 otherwise
Properties:
−1
i) SΓ = SΓ .
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ii) (Magarshak) Eigenvalues “correspond” to
Watson-Crick compatible sequences:
If we represent
Γ’s primary structure
x1
..
as x = . ∈ Qn using
xn
A 7→ i, C 7→ −1, G 7→ 1, U 7→ −i
then
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Transfer matrix: TΓ1,Γ2 = SΓ2 ◦ SΓ1
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Let us enter
Matrix model and metric
for non-W-C pairs
CMR, 2002
−1
SΓ = SΓ
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The product ∗ on Mm is defined as follows:
• ∗ is taken to be commutative;
• if λ = αl ∈ F2m , 2 ≤ l ≤ 2m − 2, then
l
z }| {
λ∗x = α ∗ (α ∗ · · · (α ∗x) · · · ) for every x ∈ Xm;
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The sum + on Mm is defined as follows:
• if β = α`m ,
a1 + u`m = u`m + a1 =a
u1 + a`m = a`m + u1 =u
u1 + g`m = g`m + u1 =u
g1 + u`m = u`m + g1 =g
g1 + c`m = c`m + g1 =g
c1 + g`m = g`m + c1 =c
x1 + k`m = k`m + x1 =x
k1 + x`m = x`m + k1 =k
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Matrix representation and metric for Cn
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Edge ideal representation and metric
for Cn
LR, 2003
Some notations:
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Given Γ = ([n], Q) ∈ Cn
πm(IΓ) = IΓ/hM(x)(m)i
∼ G(Γ) as groups if Γ ∈ U
π3(IΓ) = n
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¯ ¯
0
¯ π (I
m Γ1 )+π (I )
m Γ2 ¯
dm(Γ1, Γ2) = log2 ¯ π (I )∩π (I ) ¯¯
¯
m Γ1 m Γ2
Taking
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If Γ0 = ([n], ∅) and Γ1 = ([n], {i · j}), then
³n + m − 3´
0
dm(Γ0, Γ1) =
n
It should be 1. Thus, we normalize d0m by this
value:
dm = 1 0
dm on Cn
(n+m−3
n )
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Some computations
m = 3 on Cn:
m = 4 on Cn:
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m = 4 on Un:
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d4(Γ1, Γ2) = |Q1∆Q2| − (|Q1∆Q2| − Ω2).
n+1
m = 5 on Un:
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More info on edge ideal metrics
• If Γ1 6= Γ2, then
limm→∞
( dm(Γ1, Γ2)
0 if Γ1, Γ2 are non-empty
=
1 if either Γ1 or Γ2 is empty
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Other ideal-based representations and
metrics for Cn
JΓ ⊆ F2[x1, . . . , xn]
is generated by the set of monomials consisting
of one square-free monomial xi1 · · · xik for each
non-trivial maximal clique (maximal complete
subgraph) {i1, . . . , ik }, with k ≥ 2, of Γ.
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Given a primary structure b = b1 . . . bn and a
contact structure Γ = ([n], Q) on it, let
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Now, the ideals JΓ and KΓ can be used to
define metrics in the same way as IΓ:
¯ ¯
000
¯ πm (KΓ1 )+πm (K )
Γ2 ¯¯
dm(Γ1, Γ2) = log2 ¯ π (K )∩π (K ) ¯
¯
m Γ1 m Γ2
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Many open problems
(Some of us are working on some of them)
• Applications
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Some references: ours
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References: Others’
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