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

Abstract

A new method based on quasi-independent parallel simulation 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 the mechano-reactive kinetics than the time-averaged method typically employed to reduce the unphysical prediction of force-mediated events in BD simulations. Furthermore, the influence of the proposed replica-averaging method parameters on the accuracy of predicting the true average force profile along the polymer is discussed.