# category of molecular sets

## 0.1 Molecular sets as representations of chemical reactions

A uni-molecular chemical reaction is defined by the natural transformations

 $\eta:h^{A}\longrightarrow h^{B},$

specified in the following commutative diagram representing molecular sets and their quantum transformations:

 $\xymatrix@M=0.1pc@=4pc{h^{A}(A)=Hom(A,A)\ar[r]^{\eta_{A}}\ar[d]_{h^{A}(t)}&h^{% B}(A)=Hom(B,A)\ar[d]^{h^{B}(t)}\\ {h^{A}(B)=Hom(A,B)}\ar[r]_{\eta_{B}}&{h^{B}(B)=Hom(B,B)}},$ (0.1)

with the states of molecular sets $A_{u}=a_{1},\ldots,a_{n}$ and $B_{u}=b_{1},\ldots b_{n}$ being defined as the endomorphism sets $Hom(A,A)$ and $Hom(B,B)$, respectively. In general, molecular sets $M_{S}$ are defined as finite sets whose elements are molecules; the molecules are mathematically defined in terms of their molecular observables as specified next. In order to define molecular observables one needs to define first the concept of a molecular class variable or $m.c.v$.

A molecular class variables is defined as a family of molecular sets $[M_{S}]_{i\in I}$, with $I$ being either an indexing set, or a proper class, that defines the variation range of the $m.c.v$. Most physical, chemical or biochemical applications require that $I$ is restricted to a finite set, (that is, without any sub-classes). A morphism, or molecular mapping, $M_{t}:M_{S}\to M_{S}$ of molecular sets, with $t\in T$ being real time values, is defined as a time-dependent mapping or function $M_{S}(t)$ also called a molecular transformation, $M_{t}$.

An $m.c.v.$ observable of $B$, characterizing the products of chemical type “B” of a chemical reaction is defined as a morphism:

 $\gamma:Hom(B,B)\longrightarrow\Re,$

where $\Re$ is the set or field of real numbers. This mcv-observable is subject to the following commutativity conditions:

 $\xymatrix@M=0.1pc@=4pc{Hom(A,A)\ar[r]^{f}\ar[d]_{e}&Hom(B,B)\ar[d]^{\gamma}\\ {Hom(A,A)}\ar[r]_{\delta}&{R},}$ (0.2)

with $c:A^{*}_{u}\longrightarrow B^{*}_{u}$, and $A^{*}_{u}$, $B^{*}_{u}$ being, respectively, specially prepared fields of states of the molecular sets $A_{u}$, and $B_{u}$ within a measurement uncertainty range, $\Delta$, which is determined by Heisenberg’s uncertainty relation, or the commutator of the observable operators involved, such as $[A^{*},B^{*}]$, associated with the observable $A$ of molecular set $A_{u}$, and respectively, with the obssevable $B$ of molecular set $B_{u}$, in the case of a molecular set $A_{u}$ interacting with molecular set $B_{u}$.

With these concepts and preliminary data one can now define the category of molecular sets and their transformations as follows.

## 0.2 Category of molecular sets and their transformations

###### Definition 0.1.

The category of molecular sets is defined as the category $C_{M}$ whose objects are molecular sets $M_{S}$ and whose morphisms are molecular transformations $M_{t}$.

###### Remark 0.1.

This is a mathematical representation of chemical reaction systems in terms of molecular sets that vary with time (or $msv$’s), and their transformations as a result of diffusion, collisions, and chemical reactions.

## References

• 1 Bartholomay, A. F.: 1960. Molecular Set Theory. A mathematical representation for chemical reaction mechanisms. Bull. Math. Biophys., 22: 285-307.
• 2 Bartholomay, A. F.: 1965. Molecular Set Theory: II. An aspect of biomathematical theory of sets., Bull. Math. Biophys. 27: 235-251.
• 3 Bartholomay, A.: 1971. Molecular Set Theory: III. The Wide-Sense Kinetics of Molecular Sets ., Bulletin of Mathematical Biophysics, 33: 355-372.
• 4 Baianu, I. C.: 1983, Natural Transformation Models in Molecular Biology., in Proceedings of the SIAM Natl. Meet., Denver, CO.; Eprint at cogprints.org with No. 3675.
• 5 Baianu, I.C.: 1984, A Molecular-Set-Variable Model of Structural and Regulatory Activities in Metabolic and Genetic Networks FASEB Proceedings 43, 917.
 Title category of molecular sets Canonical name CategoryOfMolecularSets Date of creation 2013-03-22 18:16:02 Last modified on 2013-03-22 18:16:02 Owner bci1 (20947) Last modified by bci1 (20947) Numerical id 38 Author bci1 (20947) Entry type Topic Classification msc 81-00 Classification msc 18E05 Classification msc 92B05 Classification msc 18D35 Synonym class of molecular set variables and their transformations Synonym mcv-observable Related topic MolecularSetVariable Related topic MolecularSetTheory Related topic SupercategoriesOfComplexSystems Related topic ComplexSystemsBiology Related topic SupercategoryOfVariableMolecularSets Related topic IndexOfCategories Related topic CategoryOfQuantumAutomata Defines category of molecular sets Defines molecular set Defines molecular set mapping Defines states of molecular sets Defines uni-molecular chemical reaction Defines chemical transformation Defines molecular set variable Defines molecular transformation Defines $m.c.v.$ observable Defines mcv-observable Defines states of molecular se