Algebraic Modeling of Molecular Interactions

Letychevskyi, Oleksandr; Tarasich, Yulia; Peschanenko, Volodymyr; Volkov, V. A.; Sokolova, Hanna

doi:10.1007/978-3-031-14841-5_25

Cited by 3 publications

(9 citation statements)

References 13 publications

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“…Перші результати застосування алгебраїчного підходу до молекулярного моделювання були представлені в [25,26]. Початкові значення усіх атрибутів середовища (температура, тиск, магнітне поле) та атрибутів агентів задаються початковою формулою середовища та можуть бути задані як конкретно, так і символьно.…”

Section: опис підходуunclassified

Insertion semantics of quantum interactions

Tarasich,

Soloshenko

2023

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The rapid development of the chemical industry and science and new challenges in the field of health care put forward increased demands for the development of the theory of organic and inorganic chemistry, biochemistry and biophysics, the search and implementation of new modelling and analysis methods, and the improvement of technological processes. One of the safe and fast methods of researching the properties and behavior of new materials and tools is the modelling of relevant experiments, in particular, computer molecular modelling based on mathematical models. Modelling the interactions between micro and macromolecules at the quantum level allows us to manipulate the substances’ electronic, magnetic, optical and other characteristics and consider the possibilities of creating new chemical bonds, molecular structures, phase transitions, quantum states, and so on. Accordingly, the main idea of our research is to apply the technology of algebraic modelling and quantum-chemical apparatus for the simulation and verification of experiments in physics, chemistry, and biology areas. The use of formal algebraic methods allows proving properties and finding relevant scenarios for the effective analysis of the behavior of various objects in real-time, considering not individual scenarios but sets of possible behaviors. At this research stage, we have developed a methodology for formalization complex organic and inorganic substances, chemical processes and reactions based on the formalization of the interaction of atoms and molecules at the level of quantum interactions.

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Section: опис підходуunclassified

Insertion semantics of quantum interactions

Tarasich,

Soloshenko

2023

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“…For modelling, we use the Insertion Model Creator system [27][28][29], which formalizes the subject area and creates an experiment's model that will be solved in terms of formal theories . The model is then transferred to the Algebraic Server, which combines formalized mathematical theories and corresponding methods that work with models and solve problems .…”

Section: General Scheme Of the Proposed Approachmentioning

confidence: 99%

“…The precondition is determined by the predicate, which is a Boolean expression over the formulas of the corresponding theories, for example, -equality or inequality in linear arithmetic . Postcondition changes the environment and also uses predicates, assignment operators, and operations in the chosen theory [24,29,30] . Algebraic modelling is the basis of solving behavioural equations .…”

Section: General Scheme Of the Proposed Approachmentioning

confidence: 99%

“…In some cases, these may be relevant laboratory experiments, but, for example, taking into account such processes as the manufacture of drugs, we are talking about the high cost and labour-intensiveness of their implementation . We can see the solution to this problem by applying the algebraic approach and the corresponding formal methods [24] . Thus, the main idea of our research is to use the technology of algebraic modelling and quantum-chemical apparatus for modelling and verification of experiments in the field of medicine and pharmacology, in particular, modelling and verification of different approaches to the issue of investigating the properties of intercellular and intracellular interac-tions in different environments .…”

Section: Introductionmentioning

confidence: 99%

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Neurosymbolic Approach in Biological Research

Tarasich,

Soloshenko

2023

Control syst. comput.

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Modelling and studying the processes and methods of intercellular and intracellular signalling cascades regulation involved in the process of programmed cell death and searching for substances capable of influencing the activation or inhibition of the process of cell apoptosis and the methods of their transportation to a given cell, is one of the numerous actual and open issues in biological research. A safe and fast method for this that does not require research on living organisms is computer molecular modelling. Many approaches and tools have been proposed and developed in the last decade. In particular, today, we observe a wide use of analytical methods for drug creation and a search for effective treatment methods. Such methods include modern methods of artificial intelligence (AI) based on neural network technology and methods of modelling interactions in biological and chemical processes at different levels of abstraction. Neural networks are used to obtain the ligand representation, protein compounds, and others and to build predictive models of the molecular compound properties widely used in drug discovery research. Modelling methods for both continuous and discrete models are applied using various approaches: statistical, probabilistic, simulation, and visual. The most well-known and used molecular modelling methods include the docking method, the molecular dynamics method, and the Monte Carlo method. To date, many software tools that support these methods have been developed. However, the considered modelling approaches and tools have a number of disadvantages, which can be of critical importance for conducting experiments. This article presents a new approach to modelling biochemical processes and biological systems based on the formalism of the behaviour algebra and algebraic modelling language APLAN and its combination with neural network methods, the so-called Neurosymbolic approach. In particular, the possibility of multilevel modelling (from the level of the atomic structure of substances and quantum–mechanical interactions to the level of interaction of biological objects) and modelling of biological systems as complex hybrid systems that combine discrete and continuous processes is considered. A brief review of the current research on using neural network methods in biological research was also presented.

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“…The work considers the use of the theory of agents and environments based on the algebra of behaviors, which became the basis of formal methods used in modeling quantum interactions in the environment of atoms and molecules [24][25]. Based on the methodology developed by the authors for applying formal algebraic methods to the analysis of the interaction of elementary particles, attempts have been made to formalize the work of particle accelerators (Chapter 3) and the physics of the interaction of protons with substance (Chapter 4).…”

Section: програмні засоби моделювання процесів і об′єктівmentioning

confidence: 99%

Molecular modeling in the radiation therapy. The algebraic approach

Volkov

Tarasich

2022

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The rapid development of the chemical industry and science, and new challenges in the healthcare sector, put forward increased demands for the development of the theory of organic and inorganic chemistry, for the search and implementation of new modeling and analysis methods, and for the improvement of technological processes. One of the main challenges at the intersection of chemistry, physics, biol- ogy, medicine, and genetics is the search for new methods and approaches to the diagnosis and treatment of cancer. A deeper understanding of cancer’s genetics and molecular biology has led to the identification of an increasing number of potential molecular targets that can be used for the discovery and development of anticancer drugs, radiation therapy, etc. One of the main places in this is occupied by molecular modeling. Despite the availability of more and more data on existing proteins and nucleic acids and the availability of modeling methods and tools, the development and use of a wide variety of combined methods and tools for modeling and computing large molecular systems remain an open issue. One of the possible solutions for this problem is the application of the algebraic approach and the corresponding formal methods, which have proven effective in many other fields today. The main idea of the research is the application of algebraic modeling technology and quantum chemical apparatus for modeling and verification of organic chemistry problems, in particular, modeling and analysis of radiation therapy problems. The paper presents the first steps of the research. The example of the formalization of the synchrotron operation principle and the example of the interaction of protons with substance in the example of the determination/calculation of the physically absorbed dose are given in the paper.

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Algebraic Modeling of Molecular Interactions

Cited by 3 publications

References 13 publications

Insertion semantics of quantum interactions

Insertion semantics of quantum interactions

Neurosymbolic Approach in Biological Research

Molecular modeling in the radiation therapy. The algebraic approach

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