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arXiv · 2206.05851

Replica-Averaging: An algorithm to study mechano-reactive processes for polymers under flow conditions

Sagar Kania·Anh H. Nguyen·Alparslan Oztekin·Edmund Webb III
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Abstract

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.

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Sagar Kania, Anh H. Nguyen, Alparslan Oztekin, Edmund Webb III. 2022-06-12. Replica-Averaging: An algorithm to study mechano-reactive processes for polymers under flow conditions. https://doi.org/10.1063/5.0109324

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