Replica-Averaging: An algorithm to study mechano-reactive processes for polymers under flow conditions
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
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2022
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| _version_ | 1866913395835404288 |
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| author | Kania, Sagar Nguyen, Anh H. Oztekin, Alparslan Webb III, Edmund |
| author_facet | Kania, Sagar Nguyen, Anh H. Oztekin, Alparslan Webb III, Edmund |
| contents | A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This method considerably mitigates the unphysical prediction of force-mediated events inherent in Brownian dynamics (BD) polymer chain simulations that employ instantaneous force profile-based criteria to identify the occurrence of such events. This inaccuracy in predicting force-mediated event kinetics is due to high fluctuations of the instantaneous force profile around the average force. Replica-averaging reduces such high fluctuation effects by computing a force profile that faithfully represents the average force profile of the polymer chain conformation, which is then used to predict reactive events. For transient conformation conditions, the replica-averaged method more accurately predicts mechano-reactive kinetics than the time-averaged method, typically employed to reduce the unphysical prediction of force-mediated events in BD simulations. Further, the influence of the proposed replica-averaging method parameters on the accuracy of predicting the true average force profile along the polymer is discussed. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2206_05851 |
| institution | arXiv |
| publishDate | 2022 |
| record_format | arxiv |
| spellingShingle | Replica-Averaging: An algorithm to study mechano-reactive processes for polymers under flow conditions Kania, Sagar Nguyen, Anh H. Oztekin, Alparslan Webb III, Edmund Chemical Physics Soft Condensed Matter A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This method considerably mitigates the unphysical prediction of force-mediated events inherent in Brownian dynamics (BD) polymer chain simulations that employ instantaneous force profile-based criteria to identify the occurrence of such events. This inaccuracy in predicting force-mediated event kinetics is due to high fluctuations of the instantaneous force profile around the average force. Replica-averaging reduces such high fluctuation effects by computing a force profile that faithfully represents the average force profile of the polymer chain conformation, which is then used to predict reactive events. For transient conformation conditions, the replica-averaged method more accurately predicts mechano-reactive kinetics than the time-averaged method, typically employed to reduce the unphysical prediction of force-mediated events in BD simulations. Further, the influence of the proposed replica-averaging method parameters on the accuracy of predicting the true average force profile along the polymer is discussed. |
| title | Replica-Averaging: An algorithm to study mechano-reactive processes for polymers under flow conditions |
| topic | Chemical Physics Soft Condensed Matter |
| url | https://arxiv.org/abs/2206.05851 |