Dynamics of single biopolymer translocation and sedimentation

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Aalto-yliopiston teknillinen korkeakoulu | Doctoral thesis (article-based)
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Degree programme
Verkkokirja (993 KB, 78 s.)
Department of Biomedical Engineering and Computational Science publications. A, Report, 25
In this Thesis the dynamics of translocation and sedimentation of a single biopolymer (typically DNA, RNA or a protein) is studied. A coarse-graining paradigm is invoked to justify the various computational models by use of which the results are obtained. The transport of biopolymers through a nano-scale pore in a membrane is a ubiquitous process in biology. Experimental interest in translocation process focuses on its potential applicability in ultra-fast sequencing of DNA and RNA molecules. Polymer translocation has been under intense study for over a decade. Inspite of the vast theoretical research, the experimental results on the driven case have not been explained. We claim that the reason for this is that the translocation process must be treated as (at least) two dynamically distinct cases, where the dynamics takes place either close to or out of equilibrium. Here, we find that the latter case corresponds to the experiments. We make a comprehensive investigation on how the process can be discriminated based on its dynamics, and define and use some indicators to this end. In addition, we study the role of hydrodynamics, and find it to govern the dynamics when the process takes place out of equilibrium. Sedimentation is a natural process induced by gravity that can be applied experimentally in a quickened form by the use of ultracentrifuges, and which is similar to electrophoresis. Our study on behavior of single polymers under non-equilibrium conditions falls within the rapidly developing field of nano- and microfluidics that has important applications in "lab-on-a-chip" based technologies. In polymer sedimentation, we study the settling of the polymer in a steady-state in the limit of zero Péclet number, i.e. where no thermal fluctuations exist. The hydrodynamic coupling of the polymer beads leads to chaotic time-dependent behavior of the chain conformations that in turn are coupled with the velocity fluctuations of the polymer's center of mass.
Supervising professor
Kaski, Kimmo, Prof.
Thesis advisor
Linna, Riku, Dr.
polymer, translocation, dynamics, equilibrium, non-equilibrium, rheology, sedimentation
Other note
  • [Publication 1]: V. V. Lehtola, R. P. Linna, and K. Kaski. 2009. Dynamics of forced biopolymer translocation. Europhysics Letters, volume 85, number 5, 58006, 6 pages.
  • [Publication 2]: V. V. Lehtola, R. P. Linna, and K. Kaski. 2008. Critical evaluation of the computational methods used in the forced polymer translocation. Physical Review E, volume 78, number 6, 061803, 8 pages. © 2008 American Physical Society (APS). By permission.
  • [Publication 3]: V. V. Lehtola, R. P. Linna, and K. Kaski. 2010. Unforced polymer translocation compared to the forced case. Physical Review E, volume 81, number 3, 031803, 8 pages. © 2010 American Physical Society (APS). By permission.
  • [Publication 4]: V. V. Lehtola, K. Kaski, and R. P. Linna. 2010. Pore-polymer interaction reveals nonuniversality in forced polymer translocation. Physical Review E, volume 82, number 3, 031908, 6 pages. © 2010 American Physical Society (APS). By permission.
  • [Publication 5]: V. Lehtola, O. Punkkinen, and T. Ala-Nissila. 2007. Polymer scaling and dynamics in steady-state sedimentation at infinite Péclet number. Physical Review E, volume 76, number 5, 051802, 7 pages. © 2007 American Physical Society (APS). By permission.