Effective equations for reaction coordinates in polymer transport

In the framework of the problem of finding proper reaction coordinates (RCs) for complex systems and their effective evolution equations, we consider the case study of a polymer chain in an external double-well potential, experiencing thermally activated dynamics. Langevin effective equations describing the macroscopic dynamics of the system can be inferred from data by using a data-driven approach, once a suitable set of RCs is chosen. We show that, in this case, the validity of such choice depends on the stiffness of the polymer's bonds: if they are sufficiently rigid, we can employ a reduced description based only on the coordinate of the center of mass; whereas, if the stiffness reduces, the one-variable dynamics is no more Markovian and (at least) a second reaction coordinate has to be taken into account to achieve a realistic dynamical description in terms of memoryless Langevin equations.

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