On the dimensionless model of the transcription bubble dynamics
The dynamics of transcription bubbles is modeled using a system of nonlinear differential equations, the one-soliton solutions of which (kinks), are interpreted as a mathematical images of transcription bubbles. These equations contain a lot of DNA dynamic parameters, including the moments of inerti...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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AIMS Press
2023-05-01
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| Series: | AIMS Biophysics |
| Subjects: | |
| Online Access: | https://www.aimspress.com/article/doi/10.3934/biophy.2023013?viewType=HTML |
| _version_ | 1797690762808262656 |
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| author | Larisa A. Krasnobaeva Ludmila V. Yakushevich |
| author_facet | Larisa A. Krasnobaeva Ludmila V. Yakushevich |
| author_sort | Larisa A. Krasnobaeva |
| collection | DOAJ |
| description | The dynamics of transcription bubbles is modeled using a system of nonlinear differential equations, the one-soliton solutions of which (kinks), are interpreted as a mathematical images of transcription bubbles. These equations contain a lot of DNA dynamic parameters, including the moments of inertia of nitrous bases, distances between base pairs, distances from the centers of mass of bases to sugar-phosphate chains, rigidity of the sugar-phosphate backbone, and interactions between bases within pairs. However, estimates of the parameter values are often difficult, and it is not convenient or simple to operate with such multi-parameter systems. One of the ways to reduce the number of the DNA dynamic parameters is to transform the model equations to a dimensionless form. In this work, we construct a dimensionless DNA model and apply it to study transcription bubbles dynamics. We show that transformation to a dimensionless form really leads to a decrease in the number of the model parameters and really simplifies the analysis of model equations and their solutions. |
| first_indexed | 2024-03-12T02:03:49Z |
| format | Article |
| id | doaj.art-0219794fb2134db6bae8321c71b9f764 |
| institution | Directory Open Access Journal |
| issn | 2377-9098 |
| language | English |
| last_indexed | 2024-03-12T02:03:49Z |
| publishDate | 2023-05-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | AIMS Biophysics |
| spelling | doaj.art-0219794fb2134db6bae8321c71b9f7642023-09-07T06:27:28ZengAIMS PressAIMS Biophysics2377-90982023-05-0110220521910.3934/biophy.2023013On the dimensionless model of the transcription bubble dynamicsLarisa A. Krasnobaeva0Ludmila V. Yakushevich11. Siberian State Medical University, 634050 Tomsk, Moscow traсt 2, Russia 2. Tomsk State University, 634050 Tomsk, Lenin Avenue 36, Russia3. Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino. Institutskaya str. 3, Moscow region, RussiaThe dynamics of transcription bubbles is modeled using a system of nonlinear differential equations, the one-soliton solutions of which (kinks), are interpreted as a mathematical images of transcription bubbles. These equations contain a lot of DNA dynamic parameters, including the moments of inertia of nitrous bases, distances between base pairs, distances from the centers of mass of bases to sugar-phosphate chains, rigidity of the sugar-phosphate backbone, and interactions between bases within pairs. However, estimates of the parameter values are often difficult, and it is not convenient or simple to operate with such multi-parameter systems. One of the ways to reduce the number of the DNA dynamic parameters is to transform the model equations to a dimensionless form. In this work, we construct a dimensionless DNA model and apply it to study transcription bubbles dynamics. We show that transformation to a dimensionless form really leads to a decrease in the number of the model parameters and really simplifies the analysis of model equations and their solutions.https://www.aimspress.com/article/doi/10.3934/biophy.2023013?viewType=HTMLtranscription bubblenonlinear dna modelkinksmclaughlin-scott equationkink trajectories |
| spellingShingle | Larisa A. Krasnobaeva Ludmila V. Yakushevich On the dimensionless model of the transcription bubble dynamics AIMS Biophysics transcription bubble nonlinear dna model kinks mclaughlin-scott equation kink trajectories |
| title | On the dimensionless model of the transcription bubble dynamics |
| title_full | On the dimensionless model of the transcription bubble dynamics |
| title_fullStr | On the dimensionless model of the transcription bubble dynamics |
| title_full_unstemmed | On the dimensionless model of the transcription bubble dynamics |
| title_short | On the dimensionless model of the transcription bubble dynamics |
| title_sort | on the dimensionless model of the transcription bubble dynamics |
| topic | transcription bubble nonlinear dna model kinks mclaughlin-scott equation kink trajectories |
| url | https://www.aimspress.com/article/doi/10.3934/biophy.2023013?viewType=HTML |
| work_keys_str_mv | AT larisaakrasnobaeva onthedimensionlessmodelofthetranscriptionbubbledynamics AT ludmilavyakushevich onthedimensionlessmodelofthetranscriptionbubbledynamics |