Stepwise unfolding of collapsed polymers
Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, OX1 3NP, Oxford, England, UK
2 INFM and Dipartimento di Fisica “G. Galilei” dell’ Universitá di Padova, via Marzolo 8, 35131, Padova, Italy
3 The Abdus Salam Centre for Theoretical Physics, Strada Costiera 11, 34014, Trieste, Italy
4 Institut de Mathématiques B, Faculté de Sciences de Base, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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Motivated by recent experimental data on DNA stretching in presence of polyvalent counterions, we study the force-induced unfolding of a homopolymer on and off lattice. In the fixed force ensemble the globule unravels via a series of steps due to surface effects which play an important role for finite-size chains. This holds both for flexible and stiff polymers. We discuss in a qualitative way how this result may impact on the interpretation of DNA stretching experiments showing peaks in the characteristic curves, by extracting from the raw data the corresponding elongation-versus-force characteristic curves. Furthermore, approximate analytical and numerical calculations, valid in a quasi-equilibrium fixed stretch ensemble, and if the initial low-temperature state is ordered in a spool, show that the average force versus elongation displays peaks related to the geometry of the initial configuration. We finally argue how the proposed mechanisms identified for the arising of peaks may couple in the experiments, and comment on the role of dynamic effects.
© EDP Sciences, Società Italiana di Fisica, and Springer-Verlag, 2004