New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid
Abstract In this work, we proposed a new damage model for estimating radiation-induced direct damage to biomolecular systems and validated its the effectiveness for pBR322 plasmids. The proposed model estimates radiation-induced damage to biomolecular systems by: (1) simulation geometry modeling usi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-15521-y |
| _version_ | 1811224055803543552 |
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| author | Jinhyung Park Kwang-Woo Jung Min Kyu Kim Hui-Jeong Gwon Jong-Hyun Jung |
| author_facet | Jinhyung Park Kwang-Woo Jung Min Kyu Kim Hui-Jeong Gwon Jong-Hyun Jung |
| author_sort | Jinhyung Park |
| collection | DOAJ |
| description | Abstract In this work, we proposed a new damage model for estimating radiation-induced direct damage to biomolecular systems and validated its the effectiveness for pBR322 plasmids. The proposed model estimates radiation-induced damage to biomolecular systems by: (1) simulation geometry modeling using the coarse-grained (CG) technique to replace the minimum repeating units of a molecule with a single bead, (2) approximation of the threshold energy for radiation damage through CG potential calculation, (3) calculation of cumulative absorption energy for each radiation event in microscopic regions of CG models using the Monte Carlo track structure (MCTS) code, and (4) estimation of direct radiation damage to biomolecular systems by comparing CG potentials and absorption energy. The proposed model replicated measured data with an average error of approximately 14.2% in the estimation of radiation damage to pBR322 plasmids using the common MCTS code Geant4-DNA. This is similar to the results of previous simulation studies. However, in existing damage models, parameters are adjusted based on experimental data to increase the reliability of simulation results, whereas in the proposed model, they can be determined without using empirical data. Because the proposed model proposed is applicable to DNA and various biomolecular systems with minimal experimental data, it provides a new method that is convenient and effective for predicting damage in living organisms caused by radiation exposure. |
| first_indexed | 2024-04-12T08:42:33Z |
| format | Article |
| id | doaj.art-320c2a14086a4935b78ec8bb31d13293 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-12T08:42:33Z |
| publishDate | 2022-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-320c2a14086a4935b78ec8bb31d132932022-12-22T03:39:48ZengNature PortfolioScientific Reports2045-23222022-07-0112111010.1038/s41598-022-15521-yNew damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmidJinhyung Park0Kwang-Woo Jung1Min Kyu Kim2Hui-Jeong Gwon3Jong-Hyun Jung4Advanced Radiation Technology Institute, Korea Atomic Energy Research InstituteAdvanced Radiation Technology Institute, Korea Atomic Energy Research InstituteAdvanced Radiation Technology Institute, Korea Atomic Energy Research InstituteAdvanced Radiation Technology Institute, Korea Atomic Energy Research InstituteAdvanced Radiation Technology Institute, Korea Atomic Energy Research InstituteAbstract In this work, we proposed a new damage model for estimating radiation-induced direct damage to biomolecular systems and validated its the effectiveness for pBR322 plasmids. The proposed model estimates radiation-induced damage to biomolecular systems by: (1) simulation geometry modeling using the coarse-grained (CG) technique to replace the minimum repeating units of a molecule with a single bead, (2) approximation of the threshold energy for radiation damage through CG potential calculation, (3) calculation of cumulative absorption energy for each radiation event in microscopic regions of CG models using the Monte Carlo track structure (MCTS) code, and (4) estimation of direct radiation damage to biomolecular systems by comparing CG potentials and absorption energy. The proposed model replicated measured data with an average error of approximately 14.2% in the estimation of radiation damage to pBR322 plasmids using the common MCTS code Geant4-DNA. This is similar to the results of previous simulation studies. However, in existing damage models, parameters are adjusted based on experimental data to increase the reliability of simulation results, whereas in the proposed model, they can be determined without using empirical data. Because the proposed model proposed is applicable to DNA and various biomolecular systems with minimal experimental data, it provides a new method that is convenient and effective for predicting damage in living organisms caused by radiation exposure.https://doi.org/10.1038/s41598-022-15521-y |
| spellingShingle | Jinhyung Park Kwang-Woo Jung Min Kyu Kim Hui-Jeong Gwon Jong-Hyun Jung New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid Scientific Reports |
| title | New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid |
| title_full | New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid |
| title_fullStr | New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid |
| title_full_unstemmed | New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid |
| title_short | New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid |
| title_sort | new damage model for simulating radiation induced direct damage to biomolecular systems and experimental validation using pbr322 plasmid |
| url | https://doi.org/10.1038/s41598-022-15521-y |
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