Dynamics of Escape and Translocation of Biopolymers

Timo Ikonen

Research output: ThesisDoctoral ThesisCollection of Articles


The properties and dynamical behavior of polymers define and enable several processes that occur in biological systems, including the storage and duplication of genetic information in cells. Many such processes are also of considerable technological interest. For example, the driven translocation of a DNA polymer through a nano-sized pore is envisioned as a method of ultra-fast and inexpensive DNA sequencing, which may lead to revolutionary advances in medicine and biotechnology. In this dissertation, dynamics of polymers is studied in two related contexts. The first part of the thesis discusses the escape of polymers from a metastable state, which is studied with an accelerated Langevin dynamics method, the so-called Path Integral Hyperdynamics. In the same context, the method itself and its performance is studied. The results suggest that efficient separation of polymers by length or bending rigidity may be possible using external potentials. In the second part of the thesis, the driven translocation of polymers is studied. A theoretical model of the process is proposed, and its predictions are compared with molecular dynamics (MD) simulations. It is shown conclusively that the dynamics of driven translocation can be described by a two-stage process, where the polymer first straightens due to the driving force, and is thereafter effectively shortened as it threads through the pore. Furthermore, the effect of the pore and other finite size effects to the dynamical scaling of the process is discussed. Finally, driven translocation under time-dependent force is investigated with MD simulations. It is shown that for sufficiently strong attractive interactions between the pore and the polymer, the translocation becomes a thermally activated process similar to the polymer escape, and can exhibit the so-called resonant activation phenomenon. In the resonance, the translocation time attains a global minimum, which may be beneficial for, e.g., sorting and identification of polymers.
Translated title of the contributionBiopolymeerien pako- ja translokaatiodynamiikka
Original languageEnglish
QualificationDoctor's degree
Awarding Institution
  • Aalto University
  • Ala-Nissilä, Tapio, Supervising Professor
Print ISBNs978-952-60-4646-4
Electronic ISBNs978-952-60-4647-1
Publication statusPublished - 2012
MoE publication typeG5 Doctoral dissertation (article)


  • molecular dynamics
  • soft matter
  • rare events
  • polymer translocation
  • hyperdynamics
  • Resonant activation


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