Replication ratchets: polymer transport enhanced by complementarity

Abstract

We show that a rudimentary model of two complementary polymer chains confined to a quasi-one-dimensional geometry, each one interacting separately with a fixed particle via a ratchet potential, can be reformulated in terms of one polymer subject to a ratchet potential produced by its interaction with a dumbbell (or effective dimer). In the over-dampened regime, we look at transport properties when the system is under zero mean periodic external forcing. For a piece-wise linear asymmetric potential we exhibit the general mechanism by which the average mean velocity of a single polymer is enhanced by complementarity. We show that same behavior holds for a continuous ratchet potential. We relate this modelling to primitive molecular replication machines operating in outer space origin of life scenarios and argue that complementarity is not only essential to transcription but may also contribute to the efficiency of the dynamics involved in the replication process. (C) 2003 Elsevier B.V. All rights reserved.