On the hierarchy of inhomogeneous models of nonlinear dynamics of the pTTQ18 plasmid

Yakushevich L.V., Krasnobaeva L.A.
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The pTTQ18 plasmid, widely used in genetic engineering, is considered in this work as an inhomogeneous nonlinear dynamic system in which local conformation perturbations, also called open states or kinks, can arise and propagate. The pTTQ18 plasmid sequence is characterized by the presence of many functionally significant regions. Some studies use rather simple models to describe mathematically the nonlinear dynamics of plasmids, such as models containing only four functionally significant regions: promoter (Pr), terminator (Term), AmpR gene, and lacI gene. Other studies consider much more complex models, including, for example, eleven functionally significant regions: three promoters (tac promoter, lacIq promoter and AmpR promoter), two terminators (T1 and T2), two genes (lacI and AmpR), tac operator, MCS, M13 fwd and ori. Clearly, mathematical modeling the plasmid dynamic properties in this case is a much more complex task. Overall, the questions of how many and which regions should be included when constructing approximate inhomogeneous models of nonlinear plasmid dynamics remain open. When mathematically modeling the internal dynamics of the pTTQ18 plasmid, every researcher faces the question of choosing this or that approximate plasmid model. The goal of this study is to construct a hierarchy of models that could help resolve this issue. To do this, we gathered several approximate schemes of the pTTQ18 plasmid as well as models based on these schemes. Then we arranged them in order of increasing complexity, creating something like a hierarchy. For each model, we calculated the energy profile of the plasmid potential field, given that this energy profile is one of the most important characteristics reflecting the internal dynamics of the plasmid and its relationship with functional properties of the plasmid. The hierarchy constructed in this way allows researchers to navigate the flow of schemes and facilitates finding a suitable model not only for the pTTQ18 plasmid, but also for other plasmids. The hierarchy constructed in this way is the main result of the work. The proposed approach will allow researchers to better navigate the flow of pTTQ18 plasmid schemes and models, and will also facilitate the selection of an appropriate model for both pTTQ18 and other plasmids.

Keywords: plasmid pTTQ18, open states, nonlinear dynamics, kinks, hierarchy
Citation in English: Yakushevich L.V., Krasnobaeva L.A. On the hierarchy of inhomogeneous models of nonlinear dynamics of the pTTQ18 plasmid // Computer Research and Modeling, 2026, vol. 18, no. 5, pp. 1347-1364
Citation in English: Yakushevich L.V., Krasnobaeva L.A. On the hierarchy of inhomogeneous models of nonlinear dynamics of the pTTQ18 plasmid // Computer Research and Modeling, 2026, vol. 18, no. 5, pp. 1347-1364
DOI: 10.20537/2076-7633-2026-18-5-1347-1364
URL: http://crm-en.ics.org.ru/journal/article/3784/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.

Copyright © 2026 Yakushevich L.V., Krasnobaeva L.A.

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