Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива
This research delves into the essential mechanisms underlying the binding of Nitrogen (N) atoms to enzyme molecules and their implications for protein formation in food crops and biogas production. Nitrogen (N), along with Phosphorus (P) and Potassium (K), plays a pivotal role in soil fertility and...
Збережено в:
| Дата: | 2024 |
|---|---|
| Автори: | , |
| Формат: | Стаття |
| Мова: | Англійська |
| Опубліковано: |
The National Technical University of Ukraine "Igor Sikorsky Kyiv Polytechnic Institute"
2024
|
| Теми: | |
| Онлайн доступ: | https://journal.iasa.kpi.ua/article/view/322477 |
| Теги: |
Додати тег
Немає тегів, Будьте першим, хто поставить тег для цього запису!
|
| Назва журналу: | System research and information technologies |
| Завантажити файл: |  |
Репозитарії
System research and information technologies| _version_ | 1867334448139206656 |
|---|---|
| author | Matsuki, Yoshio Bidyuk, Petro |
| author_facet | Matsuki, Yoshio Bidyuk, Petro |
| author_institution_txt_mv | [
{
"author": "Yoshio Matsuki",
"institution": "World Data Center for Geoinformatics and Sustainable Development of the National Technical University of Ukraine \"Igor Sikorsky Kyiv Polytechnic Institute\", Kyiv"
},
{
"author": "Petro Bidyuk",
"institution": "Educational and Research Institute for Applied System Analysis of the National Technical University of Ukraine \"Igor Sikorsky Kyiv Polytechnic Institute\", Kyiv"
}
] |
| author_sort | Matsuki, Yoshio |
| baseUrl_str | http://journal.iasa.kpi.ua/oai |
| collection | OJS |
| datestamp_date | 2025-02-09T21:55:38Z |
| description | This research delves into the essential mechanisms underlying the binding of Nitrogen (N) atoms to enzyme molecules and their implications for protein formation in food crops and biogas production. Nitrogen (N), along with Phosphorus (P) and Potassium (K), plays a pivotal role in soil fertility and crop growth. The study explores the interactions between atoms through various mechanisms, such as catalysts, photosynthesis, and adiabatic reactions, to comprehend their roles in facilitating organic molecule formation. Additionally, the research examines the influence of enzymes on amino acids and their contributions to protein structure. The simulation process employs the Hamiltonian equation to quantify energy intensities and explore the effectiveness of adiabatic reactions in organic transformations. By investigating the molecular interactions in enzyme-catalyzed processes, this research aims to enhance protein formation in crops and optimize biogas production. |
| doi_str_mv | 10.20535/SRIT.2308-8893.2024.4.04 |
| first_indexed | 2025-07-17T10:28:39Z |
| format | Article |
| fulltext |
Publisher IASA at the Igor Sikorsky Kyiv Polytechnic Institute, 2024
Системні дослідження та інформаційні технології, 2024, № 4 55
TIДC
МАТЕМАТИЧНІ МЕТОДИ, МОДЕЛІ,
ПРОБЛЕМИ І ТЕХНОЛОГІЇ ДОСЛІДЖЕННЯ
СКЛАДНИХ СИСТЕМ
UDC 519.004.942
DOI: 10.20535/SRIT.2308-8893.2024.4.04
QUANTUM MECHANICS APPROXIMATION APPROACH
TO INVESTIGATE MOLECULAR BEHAVIOR IN NITROGEN
BINDING TO ENZYMES AND PROTEINS: IMPLICATIONS
FOR BIOFUEL PRODUCTION
YOSHIO MATSUKI, PETRO BIDYUK
Abstract. This research delves into the essential mechanisms underlying the binding
of Nitrogen (N) atoms to enzyme molecules and their implications for protein for-
mation in food crops and biogas production. Nitrogen (N), along with Phosphorus
(P) and Potassium (K), plays a pivotal role in soil fertility and crop growth. The
study explores the interactions between atoms through various mechanisms, such as
catalysts, photosynthesis, and adiabatic reactions, to comprehend their roles in facili-
tating organic molecule formation. Additionally, the research examines the influence
of enzymes on amino acids and their contributions to protein structure. The simula-
tion process employs the Hamiltonian equation to quantify energy intensities and
explore the effectiveness of adiabatic reactions in organic transformations. By inves-
tigating the molecular interactions in enzyme-catalyzed processes, this research aims
to enhance protein formation in crops and optimize biogas production.
Keywords: nitrogen binding, enzyme molecules, protein formation, adiabatic reac-
tions, biogas production, organic molecule formation.
INTRODUCTION AND BACKGROUND
Phosphorus (P), Potassium (K), and Nitrogen (N) are key elements in soil for
growing food crops. Besides the other nutrients like calcium, magnesium, and
sulfur, they form the foundation of soil and crop cultivation. Among them, Nitro-
gen is a fundamental building block for amino acids, proteins, and chlorophyll,
which are necessary for plant growth and photosynthesis, and it is a key compo-
nent of DNA, RNA, and other essential plant molecules [1].
Many organic reactions require an input of energy to overcome activation
barriers and facilitate the conversion of inorganic molecules into organic com-
pounds. This energy can be provided through various ways, including heating,
irradiation with light, or the presence of catalysts.
Proton capture is an adiabatic reaction where a proton (H+) is incorporated
into a molecule, leading to the formation of a new compound. In the process of
organic molecule formation, proton capture can occur when inorganic molecules
react with protons to form organic molecules. While proton capture can contribute
Yoshio Matsuki, Petro Bidyuk
ISSN 1681–6048 System Research & Information Technologies, 2024, № 4 56
to the adiabatic process of organic molecule formation, it is just one of several
mechanisms in the formation of organic molecule formation from inorganic pre-
cursors such as Nitrogen in inorganic form [2].
The specifics of the reactions involved in proton capture processes can vary
depending on the particular inorganic molecules and the conditions under which
they occur. Additionally, other factors such as the presence of catalysts or energy
sources can influence the efficiency and outcomes of proton capture. It is noted
that organic molecule formation is a complex and diverse field of study, and the
processes involved can be influenced by numerous factors.
Photosynthesis contributes to proton capture in amino acids indirectly by
producing NADPH (nicotinamide adenine dinucleotide phosphate oxidase) during
the light-dependent reactions. The NADPH, in turn, supplies the necessary
reducing power for the Calvin cycle, where carbon dioxide is converted into
carbohydrates, including the building block for amino acid synthesis [3].
Enzymes influence proton capture in target amino acids as catalysts.
Enzymes influence the formation of protein structure, but not by consuming itself.
The interaction happens through their electrostatic field made by the electrostatic
potentials of the atoms held by the enzyme and the targeted amino acids of the
protein [4].
Fermentation process in biogas production from wheat and maize involves
a series of physical reactions facilitated by various groups of microorganisms,
leading to the generation of biogas, which is primarily composed of methane
(CH4) and carbon dioxide (CO2) [5]. In the fermentation process of wheat/maize,
the primary microorganism involved is yeast, and the key enzyme responsible for
the conversion of sugars into ethanol (alcohol) and carbon dioxide is called
“zymase”. The typical atoms included in this enzyme are as same as in the other
enzymes’ atoms shown in Table 1 [6].
The formation of organic molecules from inorganic molecules can occur
through various processes, including biological and non-biological pathways.
While it is possible some organic reactions to occur at room temperature or under
normal conditions without external heating, the generalization that all organic
reactions can proceed adiabatically (without heat exchange with the surroundings)
or at ambient temperature is not accurate. With this research, we will estimate the
degree of the contribution to the organic molecule formation by adiabatic process
and by other processes.
RESEARCH OBJECTIVES
The primary goal of this research is to investigate the fundamental mechanism of
binding a Nitrogen atom to an enzyme molecule. The study aims to enhance pro-
tein formation in food crops and biogas production, focusing on Nitrogen in soil,
wheat, and maize crops, and the enzymes involved in their production, namely
Glutamate and Nitrate Reductase. Additionally, the research will explore the
composition of biogas production during this process, primarily consisting of me-
thane and carbon dioxide.
The main simulated physical reactions include:
1. Adiabatic Perturbation: This aims to understand the interactions between
protons and targeted atoms of the amino acids, which play a crucial role in the
binding process.
2. Electrostatic Perturbation: This analysis focuses on the influence of en-
zymes in accelerating the formation of proteins in specific targeted amino acids.
Quantum mechanics approximation approach to investigate molecular behavior…
Системні дослідження та інформаційні технології, 2024, № 4 57
3. Photon Absorption and Electron Discharge: This part examines how pho-
ton absorption leads to electron discharge from the target atom.
To quantify the energy intensities of these physical reactions in the protein
formation process involving the selected objects, the Hamiltonian equation will be
utilized.
Furthermore, this research explores the effectiveness of adiabatic reactions
in organic transformations. Specifically, it investigates whether certain organic
reactions can occur at room temperature or under normal conditions without
external heating, as this aspect is not yet clearly proven. The approximation
method in quantum mechanics will be employed to assess the possibility of
adiabatic reactions in comparison with photo synthesis and electrostatic energy
fields produced by the catalyst (enzyme) in this context.
In conclusion, this research aims to provide essential insights into the
binding of Nitrogen to enzyme molecules, which can contribute to improved
protein formation in food crops and enhance biogas production.
METHODOLOGY
Selecting typical atoms in plant tissues and enzymes. A simplified system is
considered, including typical atoms observed in wheat and maize as well as the
atoms in enzymes in these crops, as shown in Table 1.
Calculating the probability of the reactions. Each of the adiabatic pertur-
bation, electrostatic interaction, and the photon absorption, is calculated on each atom
listed in Table 1. The algorithm of the calculation is shown in the latter section.
* (the most common isotope, but there are others)
Comparing the result of the atomic level calculation with the molecular
structure. Discussion will be made on the consistency of the calculated result
with the actual molecular structure of glutamate synthetase (GS), which is essen-
tial for nitrogen uptake and assimilation from the soil. It helps convert inorganic
nitrogen compounds, such as ammonium (NH4
+) and nitrate (NO3
-), into organic
nitrogen forms like glutamate, with the following reaction [7]:
Glutamate + NH4
+ + ATP → Glutamine + Pi.
Here, glutamate is an amino acid and serves as the precursor for glutamine
synthesis. By incorporating ammonia, wheat utilizes GS to convert inorganic nitrogen
(ammonium) into the organic nitrogen compound glutamine. “Pi” is an abbrevia-
tion for “inorganic phosphate”. It refers to a form of phosphorus, an essential
element for life, which exists in the inorganic state in chemical compounds.
T a b l e 1 . Typical atoms observed in wheat and maize tissues
N
Typical atoms
in tissue
of the crops
Typical atoms
in enzymes
Atomic
number
(Number
of electrons)
Mass
number
Empirically
measured
radius (re) in
pico-meters [8]
Calculated
diameter in
pico-meters
1 Carbon (C) Carbon (C) 6 12 70 140
2 Hydrogen (H) Hydrogen (H) 1 1 25 50
3 Oxygen (O) Oxygen (O) 8 16 60 120
4 Nitrogen (N) Nitrogen (N) 7 14 65 130
5 Phosphorus (P) Phosphorus (P) 15 31* 100 200
6 Potassium (K) – 19 39* 220 440
7 Calcium (Ca) – 20 40* 180 360
8 Magnesium (Mg) – 12 24* 160 320
9 Sulfur (S) Sulfur (S) 16 32* 100 200
Yoshio Matsuki, Petro Bidyuk
ISSN 1681–6048 System Research & Information Technologies, 2024, № 4 58
Molecular form of Glutamate. The molecular formula of glutamate is
C5H9NO4. It is an organic compound composed of carbon (C), hydrogen (N), and
Oxygen (O) atoms.
ALGORITHM (HAMILTONIAN EQUATION)
Hamiltonian equation consists of 6 terms: The kinetic energy of the target proton
of amino acid, the potential of elastic electron scattering, the potential of electron
capture, the electrostatic energy of catalyst (enzyme) to influence the targeted
amino acid, and the photon absorption to drop an electron from the target amino
acid. The first term, the kinetic energy of the target proton, is set as unity, which
enables calculating relative probabilities of the occurrences of those terms.
Capture of an electron by a proton (charge exchange) in adiabatic process.
The algorithm to calculate the probability of electron capture was taken from [9].
A case was considered, in which a proton of an atom, for example Oxygen, captured
an electron of another atom, for example Hydrogen, which passed by the proton
of the atom. Fig. 1 shows the coordinates of two protons and an electron. Two
protons are symmetrically located on both sides of the origin O of the coordinate.
R)2/1( and R)2/1( are the coordinates (geometric positions) of two protons
that will capture the electron of another atom. R is the distance between two
protons, and the positions of these protons are fixed. On the other hand, r is the
position of electron in a plane polar coordinate system and it changes as a
function of geometric coordinate x , where RxR )2/1()2/1( .
Then it is assumed that the electron is initially attached to the proton at the
coordinate of R)2/1( ; then the initial state of the electron had the form,
wxRr= cos))2/1(( , where wxcos is the Eigen-wave function, w is the fre-
quency of the oscillation of the electron, representing its energy level. Then,
the probability of electron capture is calculated by the Hamiltonian equation
shown below:
wx
Rr
Cwx
R+r
CT=H e cos
)2/1(
1
cos
)2/1(
1
21
, (1)
where eT is the kinetic energy of the electron. Here, it was assumed that the rela-
tive speed of proton was much slower than the electron’s speed. Therefore, the
geometry of an electron and protons was the main focus, not time dependency of
the system. And, eT was set as a unity (one).
When the electron is attached to one proton at the coordinate of R+ )2/1( as
its initial state, the wave function is wxRr cos))2/1(( ; but, it changes to
Fig. 1. The coordinates of the proton and the electron (adapted from [9] p. 89, Fig. 21)
e(electron’s position)
0
Quantum mechanics approximation approach to investigate molecular behavior…
Системні дослідження та інформаційні технології, 2024, № 4 59
wxRr cos))2/1(( , when the electron is transferred to another proton located at
R)2/1( , as the process of the charge exchange.
The influence of enzyme to the amino acid by the electrostatic energy
[10; 11] is described by the following equation:
ij
ji
ji, ij
ji
elec r
qq
r
qq
=E
04ππ
,
where elecE is the electrostatic energy; iq and jq are the charges of the atoms;
ijr is the distance between the charges; and 0 is the vacuum permittivity.
The interaction with photon (from the interaction of a particle with the
electromagnetic field, p. 45, [9]). Under the influence of the electromagnetic field,
the momentum of a particle, p , becomes ceAp / , where e is an electron
charge, A is a vector potential of the electromagnetic field. Therefore the term of
the Hamiltonian becomes:
2mc
Ae
+Ap
mc
e
m
p
22
222
.
The first term, mp 2/2 , is eT of (1). The second term is described by only
angular coordinates, therefore we replace this term with an oscillation function
cos , where the frequency of is set higher than wx in order to simulate the
light (photon). The third term is negligibly small.
By including the terms of kinetic energy, the elastic scattering, the electron
capture, the electrostatic energy of the enzyme, and the photon absorption effect,
the Hamiltonian becomes as the follow:
wx
Rr
Cwx
R+r
CT=H e cos
)2/1(
1
cos
)2/1(
1
21
wxCwx
r
C
ji,
coscoscos
1
43 .
When the reference [9] was published in 1969, a personal computers was not
available, therefore the reference [9] further described the algorithm in mathe-
matical forms with calculus, and predicted that the squared module of the coeffi-
cients, 321 ,, CCC and 4C , gave the probability of charge exchange (the electron
capture). However, in this research a personal computer was used to calculated
the coefficients, 321 ,, CCC and 4C with the following algorithm of matrix algebra:
XTH e c ,
where X is made of four vectors, wx
Rr
cos
)2/1(
1
, wx
Rr
cos
)2/1(
1
,
wxrij cos)/(1 , wxcoscos . And c is the four column vector:
4
3
2
1
C
C
C
C
c .
Yoshio Matsuki, Petro Bidyuk
ISSN 1681–6048 System Research & Information Technologies, 2024, № 4 60
Then a constraint was set
0=HX' ,
so
0)( =XcTX' e ,
where X is transpose matrix of X. Then,
eTX'=XcX' , eTX'XX'=c 1)( .
SIMULATION PROCESS
For this simulation the values of R were assigned as the diameters of Hydrogen,
Carbon, Nitrogen, Oxygen, Phosphorus, Potassium, Calcium, Magnesium, and
Sulfur, as shown in Table 1, and r is given by (11), where x is the distance from
the origin O toward ))2/1(( R and toward ))2/1(( R in Fig. 1, while the origin
O is located at 13x : and ))2/1(( R is at 1x , and R)2/1( is at 25x .
Note: According to [9], p. 84, “Capture of an Electron by a Proton (Charge
Exchange)” of the Chap. 2.4 “Adiabatic Perturbations”, R is the distance between
the two protons of Fig. 1. Here an assumption was made as if two same atoms,
which were centered by each of two protons, were located next to each other:
therefore, rR 2 , where r is empirically measured radius of Table 1.
In our simulation for the adiabatic process, a symmetric geometry of two at-
oms was assumed as the mirror images on the both-sides of the origin O, as
shown in Fig. 2. We assign the value of R by the empirically measured radius,
25 pico-meters, for example of hydrogen-atom [10]. Because two hydrogen-atoms
are placed next to each other in Fig. 2, we assign 50 to the value of R . If charge
exchange happens, the electron’s plane polar coordinate, r , changes its position
from the initial position, 2/R of x-coordinates, to the position of the charge
exchange, R)2/1( . Then the relation between r and R is:
2
2
x
R
r
, (2)
Fig.2. Position of the electron and its coordinate r
position
Quantum mechanics approximation approach to investigate molecular behavior…
Системні дослідження та інформаційні технології, 2024, № 4 61
where x is the distance from the origin O toward R)2/1( and toward R)2/1( ,
and the origin O is at 0 on the x-axis, R)2/1( is at –12 on the x-axis; and,
R)2/1( is at +12 on
the x-axis. The electron
is initially attached to
the proton at R)2/1(
of x-coordinates; and
then it will be attached
to the proton at
R)2/1( of x-coor di-
nates after the charge
exchange.
When the nucleons
are far apart, the elec-
tron will be localized
near one or the other
proton. However, it
doesn’t mean that R in
this simulation should be
far apart to infinity, but
it only justifies the
wave functions of hy-
drogen-atom that dis-
tinguish the initial state
of the wave function
wxRr cos))2/1(( and
the wave function
wxRr cos))2/1(( af-
ter the charge exchange.
Then we set cosine
curves as the wave
functions wxcos for the
Hamiltonian equation (4).
Also, we set cos to
model the photon’s
wave function, where
frequency of cos is
higher than of wxcos
as shown in Fig. 3.
Input data for the
numeric simulation.
Then the input data were made on R , r , wxcos and wxsin as shown in Fig. 3.
The case of wxsin was also calculated during this research, but it was eliminated
from this report due to the less significance of the calculated standard error of the
coefficient.
(1) r: distance of an electron from the origin
(2) R: distance between two protons
(3) cos·wx and cos·φ
Fig. 3 Input data for the simulation: R, r, cos·wx and cos·φ
Yoshio Matsuki, Petro Bidyuk
ISSN 1681–6048 System Research & Information Technologies, 2024, № 4 62
RESULTS AND DISCUSSION
Fig. 4 and Fig. 5 illustrate the outcomes of the calculations that uncover the prob-
abilities of energy transitions between atoms through distinct mechanisms: elastic
scattering, charge exchange, catalysts, and photosynthesis. We will focus on the latter
three mechanisms, as elastic scattering involving protons is found to be negligible.
Early Stage of Wheat/Maize Growth. The insights from Fig. 4 are interest-
ing. They suggest that Nitrogen (N), Hydrogen (H), and Oxygen (O) atoms have a
unique connection with enzymes, driven by electrostatic energy. This observation
holds significance during the initial stage of wheat and maize growth. At this
juncture, enzymes like glutamate synthetase (GS), a pivotal role in converting
inorganic compounds such as ammonium (NH4
+) and nitrate (NO3
-), into organic
compounds like glutamate (C5H9NO4). These compounds lay the foundation for
the plant’s structural development.
Latter Stage of Wheat/Maize Growth by Photosynthesis. Advancing with
Fig. 4, we find Nitrogen (N) taking a central role in the adiabatic charge exchange
process, shaping the plant’s main body. Enzymes also contribute to this process, col-
laborating with Nitrogen (N). Photosynthesis, however, appears to have a gentler ef-
fect on Nitrogen (N), but exerts a more prominent influence on non-enzyme atoms
like Potassium (K). This balance reflects the rhythms of nature: photosynthesis
becomes significant after the plant has established its protein structure, while the
enzyme-driven charge exchange process takes precedence in earlier stages.
Elastic Charge exchange
Catalyst Photosynthesis
Fig. 4. Probabilities of Elastic Scattering, Charge Exchange, Catalyst Perturbation, and
Photosynthesis
Quantum mechanics approximation approach to investigate molecular behavior…
Системні дослідження та інформаційні технології, 2024, № 4 63
Fermentation Process for Biogas Production. Moving beyond growth
stages to the biogas production, Fig. 4 extends its narrative. It emphasizes the sig-
nificant roles of adiabatic charge exchange and enzyme activity in transforming
substances into methane (CH4) and carbon dioxide (CO2). Interestingly,
photosynthesis, which often occupies a prominent position in energy discussions,
appears to exert a subtler influence in the context of fermentation. These insights
deepen our understanding of how plants harness and covert energy.
Common Patterns. Revealing broader patterns, this study consistently em-
phasizes enzyme atoms as key players in the adiabatic charge exchange process.
This observation waves a coherent thread through the narrative: the orchestrated
absorption of Nitrogen (N) from the soil, contributing to the formation of plant
structures. Additionally, the impact extends beyond enzymes. Catalysts, which are
enzymes, also affect non-enzyme atoms like Potassium (K), Calcium (Ca), and
Magnesium (Mg), showing nature’s synchronized efforts to assimilate Nitrogen
(N) into plant bodies. For example, the calculated probabilities of the adiabatic
perturbation and the electrostatic perturbation on the atoms of Nitrogen (N), Hy-
drogen (H), and Oxygen (O) inspire possibilities of applying this result for further
making other enzymes that may enhance the nitrogen assimilation process.
T a b l e 2 . Calculated results and the facts (discussions)
Stage of
growth Calculated probabilities in Fig. 4 Facts
The early
stage of
wheat/
maize
growth
Each of Nitrogen (N), Hydrogen (H),
and Oxygen (O) have
the high probability of catalyst
perturbation. It means the enzyme
works well with these atoms, of the
electrostatic energy.
During the early stage of wheat/maize
growth, one of the enzymes, glutamate
synthetase (GS), helps convert inorganic
compounds, such as ammonium (NH4
+) and
nitrate (NO3
-), into organic nitrogen forms
like glutamate (C5H9NO4), which will be the
main body of the plant.
Latter
stage
of wheat/
maize
growth by
photo
synthesis
1. Nitrogen (N) has the high probabili-
ties of the adiabatic charge exchange
and the enzyme-catalyst reactions.
2. However, the probability of photo-
synthesis is negligible.
3. On the other hand, one of the
non-enzyme atoms (in the plant body
protein), Potassium (K), has the high
probability of photosynthesis.
1. The main body of the plant is formed with
the help of enzymes.
2. The photosynthesis should be effective
only after the plant forms its protein structure.
[Biol Res 43: 99-111, 2010 BR ]
3. This result is also consistent with the fact
that the photosynthesis should be effective in
forming the plant’s protein structure, while
the enzyme is to enhance the photosynthesis
of the plant proteins.
Fermen-
tation
The probability of the catalyst
perturbation is high on Carbon (C),
Hydrogen (H), and Oxygen (O),
which form methane (CH3) and
carbon dioxide (CO2).
The probability of adiabatic charge
exchange is also large on these atoms
Fermentation process in biogas production
from wheat and maize involves a series of
physical reactions facilitated by various
groups of microorganisms, leading to the
generation of biogas, which is primarily com-
posed of methane (CH4) and carbon dioxide
(CO2).
Conclu-
sion
The calculated results suggest that
Nitrogen is notably influenced by
adiabatic charge exchange and the
enzyme-catalyzed reactions.
“Nitrogen fixation” is facilitated by enzymes
and proteins through an adiabatic process
without the need for heating, accompanied by
photon absorption, which enhances the for-
mation of robust protein structures.
Yoshio Matsuki, Petro Bidyuk
ISSN 1681–6048 System Research & Information Technologies, 2024, № 4 64
CONCLUSION AND RECOMMENDATION
In light of the comprehensive investigation into the mechanisms governing the
binding of Nitrogen (N) atoms to enzyme molecules and their implications for protein
formation in food crops and biogas production, several key insights emerge.
Enhancing Protein Formation in Food Crops: The study’s findings shed
light on the intricate interactions occurring during the early and latter stages of
wheat and maize growth. The high probabilities of catalyst perturbation, as indi-
cated by the analysis, suggest that enzymes effectively collaborate with Nitrogen
(N), Hydrogen (H), and Oxygen (O) atoms. Particularly during the initial growth
stages, enzymes such as glutamate synthetase (GS) facilitate the conversion of
inorganic compounds into organic nitrogen forms like glutamate, which contrib-
utes to the formation of the plant’s structural components. These insights not only
deepen our understanding of protein formation but also hold potential for optimiz-
ing crop growth strategies.
Biogas Production Optimization: For the fermentation process aimed at
biogas production, the observation highlights the important role of enzyme atoms
in both the adiabatic charge exchange process and the catalytic effects of enzymes
in promoting methane (CH4) and carbon dioxide (CO2) production. These factors
are crucial contributors to efficient biogas generation. Importantly, the limited
influence of photosynthesis on the fermentation process suggests that the latter
stages of plant growth are more relevant to biogas production. This understanding
could aid in refining biogas production processes, potentially leading to increased
energy yield from agricultural products.
Adiabatic Charge Exchange and Enzyme-Catalyst Dynamics: The re-
search consistently highlights the role of the adiabatic charge exchange process,
particularly concerning Nitrogen (N) assimilation into plant structures. This corre-
sponds to the process of constructing the fundamental elements of plants by absorbing
Nitrogen (N) from the soil. Additionally, the interplay between catalysts (enzymes)
and non-enzyme elements such as Potassium (K), Calcium (Ca), and Magnesium
(Mg) highlights how enzymes play a significant role in aiding the incorporation of
Nitrogen (N) into plant structures, aligning with anticipated outcomes.
Ethical Consideration and Future Implications: Beyond the calculated re-
sults, these findings encourage us to ponder ethical dimensions. The concept of
genetically enhancing enzymes for improved biogas production emerges as a
guiding principle, as indicated by the Quantum Mechanics Approximation Ap-
proach. Unlike the heated debates surrounding genetic engineering in food crops
this pathway appears to encounter fewer ethical challenges. The fusion of scien-
tific understanding and ethical contemplation points to a fresh direction in opti-
mizing biogas production.
Recommendation: As each calculated probability unveils the narrative of
atomic interactions, the study’s conclusions prompt us to take actionable steps.
Guided by these insights, it is essential for the scientific community to initiate
practical applications. Validating these findings through experiments in actual
agricultural and biogas production settings could pave the way for transformative
breakthroughs. Collaboration among mathematicians, molecular biologists, agri-
cultural experts, and careful environmental management opens avenues to a future
where mathematical analysis, innovation, and ethical considerations converge to
address urgent needs in sustainable agriculture and renewable energy. In conclud-
ing this mathematical exploration, the symphony of intricate atomic interactions
resonates. Beyond mathematical harmonic, we catch a glimpse of a world where
ethical considerations intertwine harmoniously with exploration, guiding us to-
ward a future enriched by mathematical inquiry, innovation and ethical guidance.
Quantum mechanics approximation approach to investigate molecular behavior…
Системні дослідження та інформаційні технології, 2024, № 4 65
REFERENCES
1. S.J. Parikh, B.R. James, “Soil: The Foundation of Agriculture,” Nature Education
Knowledge, 3(10):2, 2012. Available: https://www.nature.com/scitable/knowledge/ li-
brary/soil-the-foundation-of-agriculture-84224268/
2. Agostino Migliore, Nicholas F. Polizzi, Michael J. Therien, and David N. Beratan, “Bio-
chemistry and Theory of Proton-Coupled Electron Transfer,” Chem. Rev., 2014, 114,
pp. 3381−3465. Available: https://pubs.acs.org/doi/pdf/10.1021/cr4006654
3. B. Alberts et al., Molecular Biology of the Cell; 4th edition. New York: Garland Science,
2002. Available: https://www.ncbi.nlm.nih.gov/books/NBK26819/
4. António J.M. Ribeiro, Jonathan D. Tyzack, Neera Borkakoti, Gemma L. Holliday, and
Janet M. Thornton, “A global analysis of function and conservation of catalytic residues
in enzymes,” J. Biol. Chem., 295(2), pp. 314–324, 2019. doi: 10.1074/jbc.REV119.006289
5. P. Weiland, “Biogas production: current state and perspectives,” Appl. Microbiol. Bio-
technol., 85, pp. 849–860, 2010. doi: 10.1007/s00253-009-2246-7
6. D.C. Phillips, “The Three-dimensional Structure of an Enzyme Molecule,” Scientific
American, November 1966. Available: https://web.ics.purdue.edu/~gchopra/class/ pub-
lic/readings/Introduction_Lecture1/Phillips_SCIAM_66_Lysozyme_ structure.pdf
7. M. Spodenkiewicz, C. Diez-Fernandez, V. Rüfenacht, C. Gemperle-Britschgi, and J. Häberle,
“Minireview on Glutamine Synthetase Deficiency, an Ultra-Rare Inborn Error of Amino
Acid Biosynthesis,” Biology 5(4), 40, 2016. doi:10.3390/biology5040040
8. J.C. Slater, “Atomic Radii in Crystals,” J. Chem. Phys., 41, 3199, 1964. doi:
https://doi.org/10.1063/1.1725697
9. A.B. Migdal, V. Krainov, Approximation Methods in Quantum Mechanics; translated by
Anthony J. Leggett, New York: W.A. Benjamin Inc., 1969, 146 p.
10. Vinicius de Godoi Contessoto et al., “Electrostatic interaction optimization improves
catalytic rates and thermotolerance on xylanases,” Biophys. J., 120(11), pp. 2172–2180,
2021. doi: 10.1016/j.bpj.2021.03.036
11. R.P. Feynman, R.B. Leighton, and M. Sands, Thy Feynman Lectures on Physics; Vol. II
Ch. 4: Electrostatic Energy. New Millennium edition, 2011, 1552 p. Available:
https://www.feynmanlectures.caltech.edu/II_08.html
Received 23.08.2023
INFORMATION ON THE ARTICLE
Yoshio Matsuki, ORCID: 0000-0002-5917-8263, World Data Center for Geoinformatics
and Sustainable Development of the National Technical University of Ukraine “Igor Si-
korsky Kyiv Polytechnic Institute”, Ukraine, e-mail: matsuki@wdc.org.ua
Petro I. Bidyuk, ORCID: 0000-0002-7421-3565, Educational and Research Institute for
Applied System Analysis of the National Technical University of Ukraine “Igor Sikorsky
Kyiv Polytechnic Institute”, Ukraine, e-mail: pbidyuke_00@ukr.net
АПРОКСИМАЦІЙНИЙ ПІДХІД КВАНТОВОЇ МЕХАНІКИ ДЛЯ ДОСЛІДЖЕННЯ
МОЛЕКУЛЯРНОЇ ПОВЕДІНКИ ЗВ’ЯЗУВАННЯ АЗОТУ З ФЕРМЕНТАМИ ТА
БІЛКАМИ: ЗНАЧЕННЯ ДЛЯ ВИРОБНИЦТВА БІОПАЛИВА / Й. Мацукі, П.І. Бідюк
Анотація. Це дослідження заглиблюється у суттєві механізми зв’язування
атомів азоту (N) з молекулами ферментів та їх наслідки для утворення білків у
харчових культурах та виробництві біогазу. Азот, разом з фосфором (P) та ка-
лієм (K), відіграє важливу роль у родючості ґрунту та рості врожаю. Дослі-
джено взаємодії між атомами за допомогою різних механізмів, таких як каталі-
затори, фотосинтез та адіабатичні реакції, для розуміння їх ролей у полегшенні
утворення органічних молекул. Додатково досліджено вплив ферментів на
амінокислоти та їх внесок у структуру білків. Процес симуляції використовує
рівняння Гамільтона для кількісної оцінки інтенсивності енергії та досліджен-
ня ефективності адіабатичних реакцій у органічних перетвореннях. Через до-
слідження молекулярних взаємодій у фермент-каталізованих процесах це до-
слідження спрямоване на поліпшення утворення білків у врожаях та
оптимізацію виробництва біогазу.
Ключові слова: зв’язування азоту, молекули ферментів, утворення білків, аді-
абатичні реакції, виробництво біогазу, утворення органічних молекул.
|
| id | journaliasakpiua-article-322477 |
| institution | System research and information technologies |
| keywords_txt_mv | keywords |
| language | English |
| last_indexed | 2025-07-17T10:28:39Z |
| publishDate | 2024 |
| publisher | The National Technical University of Ukraine "Igor Sikorsky Kyiv Polytechnic Institute" |
| record_format | ojs |
| resource_txt_mv | journaliasakpiua/9c/6d9658cca25ef9d46f812da25bf2679c.pdf |
| spelling | journaliasakpiua-article-3224772025-02-09T21:55:38Z Quantum mechanics approximation approach to investigate molecular behavior in nitrogen binding to enzymes and proteins: Implications for biofuel production Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива Matsuki, Yoshio Bidyuk, Petro зв’язування азоту молекули ферментів утворення білків адіабатичні реакції виробництво біогазу утворення органічних молекул nitrogen binding enzyme molecules protein formation adiabatic reactions biogas production organic molecule formation This research delves into the essential mechanisms underlying the binding of Nitrogen (N) atoms to enzyme molecules and their implications for protein formation in food crops and biogas production. Nitrogen (N), along with Phosphorus (P) and Potassium (K), plays a pivotal role in soil fertility and crop growth. The study explores the interactions between atoms through various mechanisms, such as catalysts, photosynthesis, and adiabatic reactions, to comprehend their roles in facilitating organic molecule formation. Additionally, the research examines the influence of enzymes on amino acids and their contributions to protein structure. The simulation process employs the Hamiltonian equation to quantify energy intensities and explore the effectiveness of adiabatic reactions in organic transformations. By investigating the molecular interactions in enzyme-catalyzed processes, this research aims to enhance protein formation in crops and optimize biogas production. Це дослідження заглиблюється у суттєві механізми зв’язування атомів азоту (N) з молекулами ферментів та їх наслідки для утворення білків у харчових культурах та виробництві біогазу. Азот, разом з фосфором (P) та калієм (K), відіграє важливу роль у родючості ґрунту та рості врожаю. Досліджено взаємодії між атомами за допомогою різних механізмів, таких як каталізатори, фотосинтез та адіабатичні реакції, для розуміння їх ролей у полегшенні утворення органічних молекул. Додатково досліджено вплив ферментів на амінокислоти та їх внесок у структуру білків. Процес симуляції використовує рівняння Гамільтона для кількісної оцінки інтенсивності енергії та дослідження ефективності адіабатичних реакцій у органічних перетвореннях. Через дослідження молекулярних взаємодій у фермент-каталізованих процесах це дослідження спрямоване на поліпшення утворення білків у врожаях та оптимізацію виробництва біогазу. The National Technical University of Ukraine "Igor Sikorsky Kyiv Polytechnic Institute" 2024-12-25 Article Article application/pdf https://journal.iasa.kpi.ua/article/view/322477 10.20535/SRIT.2308-8893.2024.4.04 System research and information technologies; No. 4 (2024); 55-65 Системные исследования и информационные технологии; № 4 (2024); 55-65 Системні дослідження та інформаційні технології; № 4 (2024); 55-65 2308-8893 1681-6048 en https://journal.iasa.kpi.ua/article/view/322477/312891 |
| spellingShingle | зв’язування азоту молекули ферментів утворення білків адіабатичні реакції виробництво біогазу утворення органічних молекул Matsuki, Yoshio Bidyuk, Petro Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива |
| title | Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива |
| title_alt | Quantum mechanics approximation approach to investigate molecular behavior in nitrogen binding to enzymes and proteins: Implications for biofuel production |
| title_full | Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива |
| title_fullStr | Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива |
| title_full_unstemmed | Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива |
| title_short | Апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: Значення для виробництва біопалива |
| title_sort | апроксимаційний підхід квантової механіки для дослідження молекулярної поведінки зв’язування азоту з ферментами та білками: значення для виробництва біопалива |
| topic | зв’язування азоту молекули ферментів утворення білків адіабатичні реакції виробництво біогазу утворення органічних молекул |
| topic_facet | зв’язування азоту молекули ферментів утворення білків адіабатичні реакції виробництво біогазу утворення органічних молекул nitrogen binding enzyme molecules protein formation adiabatic reactions biogas production organic molecule formation |
| url | https://journal.iasa.kpi.ua/article/view/322477 |
| work_keys_str_mv | AT matsukiyoshio quantummechanicsapproximationapproachtoinvestigatemolecularbehaviorinnitrogenbindingtoenzymesandproteinsimplicationsforbiofuelproduction AT bidyukpetro quantummechanicsapproximationapproachtoinvestigatemolecularbehaviorinnitrogenbindingtoenzymesandproteinsimplicationsforbiofuelproduction AT matsukiyoshio aproksimacíjnijpídhídkvantovoímehaníkidlâdoslídžennâmolekulârnoípovedínkizvâzuvannâazotuzfermentamitabílkamiznačennâdlâvirobnictvabíopaliva AT bidyukpetro aproksimacíjnijpídhídkvantovoímehaníkidlâdoslídžennâmolekulârnoípovedínkizvâzuvannâazotuzfermentamitabílkamiznačennâdlâvirobnictvabíopaliva |