Beruflich Dokumente
Kultur Dokumente
Luciana Morogan
No Institute Given
Abstract. abstract
1 Prerequisites
The length of the string of objects obtained by deleting from x of all symbols
not in U, U ⊆ O is denoted |x|U and
X
|x|U = |x|a .
a∈U
The last working definition given here is that of the Parikh vector of x associated
with alph(x) for alph(x) = {a1 , a2 , . . . , an } , n ∈ IN+ (the order of a1 , a2 , . . . , an
is arbitrary but fixed, we may say that some order it is chosen, no matter which
one) is defined as the function ψalph(x) : O∗ → INn ,
notation
|O|a ∈ IN represents the number of copies of a in O. If |O|a = ∗, then we
say that the object a is found in an arbitrary number of copies.
with ψalph(x) (x) = (|x|a1 , |x|a2 , . . . , |x|an ) and Sn the set of all permutations
of n elements. If we choose any permutation π ∈ Sn then we define a map-
not
ping fπ : On → On such as fπ (a1 . . . an ) = aπ(1) . . . aπ(n) = y, y ∈ O∗ with
ψalph(y) (y) = (|y|a1 , |y|a2 , . . . , |y|an ) (y is a permutation of x). As alph(x) =
alph(y), (ψalph(x) (y) = (|y|a1 , |y|a2 , . . . , |y|an )) and (|x|a1 , |x|a2 , . . . , |x|an ) =
(|y|a1 , |y|a2 , . . . , |y|an ) (y is a permutation of x) we have that ψalph(x) (x) =
ψalph(y) (y). So, if Mx = {(a1 , |x|a1 ), (a2 , |x| a2 ), . . . (an , |x|an )} and My = (aπ(1) ,
|y|aπ(1) ), (aπ(2) , |y|aπ(2) ), . . . (aπ(n) , |y|aπ(n) ) and y is obtained by a permutation
of x, then Mx = My . We may say that permutations of the same string x ∈ O∗
are describing exactely the objects in the support of M and their multiplicities
(permutations of the same sting are describing exactley the same multiset over
O).
We will represent the multiset M = {(a1 , M (a1 )), (a2 , M (a2 )), . . . , (an , M (an ))},
M (a ) M (a ) M (a )
with alph(M ) = {a1 , . . . , an }, as the string a1 1 a2 2 . . . an n .
such as M (ai ) > 0 and ψalph(x) (x) = (|x|a1 , . . . , |x|an ) the finite alphabet of
multiset M (one may say the support of M ). Generally, we can consider that
S ⊆ O∗ is interpreted as the multiset defined by
∀x ∈ S, S(x) = 1
∀x ∈
/ S, S(x) = 0
M (x ) M (x ) M (x )
as a string of the form x1 1 x2 2 . . . xn n , for alph(M ) = {x1 , . . . , xn }
and the multiplicities of the objects in the support M (x1 ), M (x2 ), . . . , M (xn ).
All permutations of this string identfie objects in the support (alphabet) of M
and their multiplicities. For two multisets M1 and M2 the inclusion, union and
difference between them are defined as above.
Example 3. The string (ab)3 (abb)2 (aa)∗ describes the multiset of string objects
containing three copies of ab, two copies of abb and an arbitrary number of copies
of aa. Here, alph(M ) = {ab, abb, aa} ∪ {(, )}, where the paranteses are used for
a better representation of string molecules in M .
such as
not
– there is r1 , r2 , ..., rp ∈ {1, ..., k1 }, 1 ≤ p ≤ k1 with ir1 = ir2 = ... = irp = ir
– for all j ∈ {1, ..., k1 } with j 6= rl for all l ∈ {1, ..., p} we have ij 6= irl
5
where
We will denote the set [M ]∗⇒ = {x2 ∈ Mk2 | there is (x1 , x2 ) ∈ Mk1 × Mk2 for
k1 ≥ k2 and Mk1 , Mk2 ∈ [M ]∗ such as for all x1 ∈ Mk2 , x1 ⇒ x2 }. The set [M ]∗⇒
is called the Compounds Domain and, to simplify the writing, from now on
we will refear to it by the notation CD.
M (a ) M (a2 )
Example 4. To illustrate what we wrote above, let‘s take two strings a1 1 1 , a2 1 ∈
M (a ) M (a )
M1 . Under the concatenation, a new string a1 1 1 a2 1 2 is formed in M2 . An-
M1 (a1 ) M (a ) M (a )
other example: taking the string objects a1 ∈ M1 and a1 2 1 a2 2 2 ∈
M (a ) M (a ) M (a )
M2 , a new formed strig a1 1 1 a1 2 1 a2 2 2 from M3 can be rewrited in
M1 (a1 )+M2 (a1 ) M2 (a2 )
a1 a2 in M2 .
M1 /x → M1new /y
where:
n
M (a ) M (a ) M (a ) M (a ) M (a )
– if M1 = a1 1 , ..., ai1 i1 , ..., ai2 i2 , ..., aim im , ...an n |∀k ∈ {1, ..., n} ,
ak ∈ alph(M1 ), alph(M1 ) = {a1 , ..., an }} and x = (aji11 , aji22 , ..., ajim
m
) for jk ∈
j1 j2 jm
IN, 0 ≤ jk ≤ M (aik ) then y = ai1 ai2 ...aim and
n o
M (a ) M (a )−j M (a )−j M (a )−j M (a )
– M1new = a1 1 , ..., ai1 i1 1 , ..., ai2 i2 2 , ..., aim im m , ...an n
M1 /y → M1new /x
where:
n
M (a ) M (a ) M (a ) M (a ) M (a )
– if M1 = a1 1 , ..., ai1 i1 , ..., ai2 i2 , ..., aim im , ...an n |∀k ∈ {1, ..., n} ,
ak ∈ alph(M1 ), alph(M1 ) = {a1 , ..., an }} and y = aji11 aji22 ...ajim
m
then x =
j1 j2 jm
(ai1 , ai2 , ..., aim ) for jk ∈ IN, 0 ≤ jk ≤ M (aik ) and
n o
M (a ) M (a )+j M (a )+j M (a )+j M (a )
– M1new = a1 1 , ..., ai1 i1 1 , ..., ai2 i2 2 , ..., aim im m , ...an n
molecule a3 c5 is obtained by applying the rule M1 /(a3 , c5 ) → M1new /a3 c5 with
M1new = b2 , c∗ . At the decomposition of the molecular formula a3 c5 , if we
3 5 new 3 5
new new 6 2 ∗
c → M1 /(a , c ) is applied
suppose the initial content of M1 , therule M1 /a
and the content of M1 is M1 = a ,b ,c .
SI = {y ∈ CD| there is x ∈ Mk1 × ... × Mkn for any k1 , ..., kn ∈ {1, ..., n}
for k ∈ {1, ..., n}}.
We will use a set P3 of rules that attach a spatial orientation (of atoms/groups
of atoms in its constitution) to a compound from SII . The universal alphabet of
8
all possible spatial configurations of objects is Γ . As our work has its inspiration
in biology where the spatial arrangement of atoms/groups of atoms in a real
molecule is finite (for example, there are only a few possiblities of different protein
spatial conformations), the term universal alphabet is used here to refear to all
three-dimensional structure of all molecules object compound types. So, Γ is the
set of all three-dimensional structures molecules, the spatial arrangements of the
secondary structures of molecules in SII and we will refear to it as the set of all
spatial configurations.
Let it be Γ = {Γ1 , Γ2 , ..., Γq }, where q ∈ IN, q fixed. Γ ∗ is the set of all possible
strings of configurations under the operation of concatenation. A rule in P3 has
the form (u, v) ∈ P3 with P3 ⊆ SII × Γ ∗ and we denote it by the symbol |=SII .
We write that
for all u ∈ SII there is v ∈ Γ ∗ such as u |=SII (u|v).
So, we have
for all u ∈ SII , u = (y|z) there is v ∈ Γ ∗ such as (y|z) |=SII (y|z|v).
We define, this way,
SIII = {(y|z|v)| for all y ∈ SI , y `SI z there is v ∈ Γ ∗ such as
(y|z) |=SII (y|z|v)}.
This hierarchy of construction of the complex language of objects molecules
(componds or complexes) can be graphically represented in the figure below.