Computer as chemical reactor

UDC 004
Publication date: 30.09.2019
International Journal of Professional Science №9-2019

Computer as chemical reactor

Ivanov N.V., Pronkin N.N.
First Moscow State Medical I.M. Sechenov University of the Ministry of Healthcare of the Russian Federation (Sechenov University), Moscow, Russia
Abstract: The article proposes detailed analogues between (Enzyme – Substrate) and (Program – Data) complexes.
It reveals great amount of analogues basing of information technology and molecular biology.
The concept brain as computer is critiqued. It looks like biological cell as computer is more powerful and close to true.
Keywords: Enzyme; substrate; computer program, data.

The new concept is offered —computer as chemical reactor”, in which, at one task regime of work, is carried out unique enzyme reaction.

Let us given enzymatic reaction, a standard kind:

E + S ⇄ ES ⇄ ES* ⇄ EP ⇄ E + P

We shall consider Е (enzyme) — as the computer program, S (substrate) — as the initial data, P (product) — as a result of work of the program. It is possible to be convinced of existence of analogy between Enzyme — Substrate interaction and interaction of Program (E) — Data (S).

Firstly, the program, as well as enzyme, is used repeatedly, many times.

Secondly, the program, as well as enzyme, accelerates processing S:

If enzyme accelerates reaction SP in a solution (without enzyme), the program accelerates processing of the initial data in comparison with the calculating «Manually».

In thirdly, product (P) in its turn can be substrate for next enzyme reaction (another program).

This approach differs from one offered by E.A. Liberman [5, 6] that

  1. The program considers enzyme, instead of DNA, as in E.A. Liberman’s works.
  2. The minimal word — the letter at E.A. Liberman is cАМP, at our proposal these are atoms of enzyme, or mRNA.
  3. Our approach specifies concrete conformity between processes of transformations of substance and the information, and structures, in these  processes participating.

 If more deeply to look after analogy between Enzyme — Substrate interaction and interaction of Program (E) — Data (initial S, result — P), considering concepts and processes of molecular biology [7 — 9] it is possible to establish great amount of mutually — unequivocal conformity (see. Table 1).

Table 1. The table of analogies (Enzyme – Substrate)  and (Program – Data)


Enzyme — Substrate a complex → the Complex  Program – Data

(transformation of substance) → (transformation of the information)


  1. Enzyme → 1. Program in machine codes

Turns of enzyme → Runs of program

  1. Substrate → 2. The entrance data in decimal system
  2. Product → 3. The target data in decimal system
  3. Activated complex → 4. The data in binary system + program in codes
  4. Translation of mRNA to protein → 5. Compilation of program
  5. Genes of enzyme in mRNA → 6. Program in high-level language (e.g. JAVA)
  6. Mutations in mRNA → 7. Change program to JAVA
  7. DNA → 8. Algorithm
  8. Mutations in DNA → 9. Change of algorithm
  9. A ribosome → 10. Compiler
  10. Transcription DNA into mRNA → 11. Writing of program by algorithm
  11. Types of atoms mRNA → 12. Digits, letters in decimal system
  12. Types of atoms of enzyme → 13. Digits, letters in binary system
  13. Chemical bonds → 14. Formulae, connecting digits, letters
  14. Codon (triplet of nucleotides) →15. A symbol one of 256 alphanumeric ASCII
  15. Amino acid → 16. Byte (an octet of bits)
  16. A genetic code — conformity codon → Аmino Acid → 17. Conformity byte → symbol
  17. Active centre (AC) of enzyme → 18. Operators, transforming the data

Parallel calculations

 а) A few AC at enzyme → а) inside one program

  1. b) A few enzymatic reactions→ b) multitask, multiuser regime
  2. Topochemical conformity (E-S) →19. Conformity of input formats of the data to

formats of input operators

  1. Inhibition by Substrate analogue → 20. A stop program because of discrepancies of input data

to program’s requests

  1. Splicing of RNA→21. Erasing from comments after compiling
  2. Intron, exon → 22. Comment, operator
  3. Virus embedding in gene → 23.—Is absent
  4. Inactivation of enzyme → 24. Virus, affected *.exe, *.com files
  5. Immunoglobulines → 25. Programs-antiviruses
  6. Processing of enzyme → 26. Editoring connections (LinkEditor)
  7. Compartments → 27. Directories and subdirectories
  8. Organelles → 28. Disk drives A, B, C…..
  9. A cell → 29. Computer
  10. Media, in which enzymatic reaction take place → 30. Processor, a site of RAM with which

a program works

  1. Coordination of all processes in a cell → 31. Work of OS
  2. A tissue, multycellular organism → 32. A network of computers


REMARK on point) 23: This unique «discrepancy» in the given table.

To explain this it is possible for that algorithms with superfluous steps and with mistakes are edited. Anyway they are not multiplied. If to algorithm A the virus B «will be pasted» the final algorithm А+В will be longer then initial one. The basic criterion of selection of optimal algorithm is it shortness. Obviously criterion of selection for DNA is another since the fact of redundancy of the information in DNA is well-known.

Such way, in the frame of proposed concepts computer looks not a brain, but only one biological cell, so the name «neurocomputer» (instead of braincomputer) appears rather successful.

Concerning the concept «a brain — as computer». From an authors’s point of view analogy between a brain and computer is rather formal [1 — 4]; with the same success it is possible to compare a brain with radio tuner, which too transforms information, has inputs — outputs, switching and nonlinear elements, «synaptic» lags etc. Moreover, in tuner it is solved a problem of allocation of a signal from noise, which the brain is solved, but which at usual work of computer does not arise.

The brain can work as a computer. The converse statement, generally speaking, is not true. Because a computer is much simpler than a brain. Though, certainly, complexity depends on a level of detailed elaboration. If to consider behaviour of separate electrons, the computer can be more complex than a brain as system of neurons. But we consider information aspects of work of a computer at the level of detailed elaboration submitted in Table 1.

What the above mentioned analogy gives?

First, the generality such, would seem far areas as processing of the information and molecular biology, specifies existence of certain general principles.

Principles of transformation of substance and the information are identical.

  1. Generalized ES — principle: Transformation as substances, and information S is at many times using of slowly — varying (in comparison with S) structure
  2. A principle of reciprocity: at processing the information the substance is used, and at processing of substance — the information is used; the information is inseparable from its material carrier — substance.
  3. A principle of intermediate structure. For greater reliability between DNA and protein it is placed mRNA, and between algorithm and the executed program — the program in high-level language (e.g. JAVA).

Moreover, it is possible to assume, that the human organism can not think up something (a computer, programs, the information) essentially distinguished from himself (cells, genes, enzymes).

Second, univocal conformity between two areas to each of them it is possible to apply a rich arsenal of the means advanced for other area so far as is established. For example, well developed mathematical methods for the analysis enzyme kinetics [10-12] it is possible to apply for the analysis of efficiency of computer program. And vice versa — methods and tools, developed in computer technologies, starting from  microelectronics [13], estimations and optimization of programs [14,15] And finishing developing of algorithms [16] are possible to use in enzyme kinetics and molecular biology.

Thirdly, proceeding from results on second point, it is possible to solve a bionics task: to create a computer on molecular-biological principles. The initial data — it is artificial synthesized substrate, the Program — the enzyme processing given substrate. The basic problem of such enzyme computer — decoding of the final results which have been «written down» as a molecule of a product of reaction.

From the point of view of the authors it will be possible only with application of a laser.

In — fourth, it is possible to predict evolution of computers since courses and rules of biological evolution in general to us are known. It is possible to propose, that the further developing of computer engineering will go on a way of specialization of «tissues»: allocation of certain «types» in computer networks. Such «clones» of computers will win, which faster than others will solve a global task of capture of space.


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