Single Polymer Dynamics in Confined Geometries: Capsid Ejection and Sedimentation

Joonas Piili

Research output: ThesisDoctoral ThesisCollection of Articles


Polymer physics has inspired scientists partly because by using fairly general statistical physics models, one can gain understanding on the most fundamental aspects of life. The polymer models, some of which are even analytically solvable, can be used to describe characteristics of DNA, RNA, and proteins to a good precision. In this thesis, we use coarse-grained simulations for studying the general dynamics of sedimentation of knotted polymers and capsid ejection. Sedimentation and electrophoresis are standard tools used in DNA research. Capsid ejection is vital in understanding how viruses of certain type function. In sedimentation the polymer is moved through a fluid by gravitational force. We study how the knot topology of such polymers reflect the sedimentation velocity. Using a direct model that makes no assumptions of the polymer conformation or its interaction with the fluid we find that there is a linear relationship between the sedimentation velocity and the average crossing number of the knot topology to a good precision. The reason is that the radius of gyration of the knotted polymer is inversely proportional to its average crossing number. When sedimentation is modeled in a slit strongly restricting the polymer's conformation, the linear relation between sedimentation velocity and average crossing number is sustained, albeit it is not as precise as in free solvent. In capsid ejection a polymer, initially densely packed inside a spherical capsid, escapes through a narrow pore. In this thesis, no external forces are applied, but the ejection is driven only by the polymer's internal pressure and entropy difference. We study different aspects and dynamic regimes relevant for the ejection dynamics. We find that the semidilute assumption often used to theoretically describe the ejection dynamics of flexible polymer chains is not valid when starting the ejection from strong confinement. More precisely, in strong confinement the monomer-monomer interactions become dominant. This shows in the force at the pore increasing exponentially with the number of monomers inside the capsid. This is reflected on the ejection dynamics. The cumulative waiting times, i.e., the time it takes for each monomer to eject the capsid, increases exponentially with the number of ejected beads. Hydrodynamic interactions are always present in real-world capsids as the natural polymers reside in aqueous solutions. We characterize the effects of hydrodynamics in capsid ejection. We find that while the inclusion of hydrodynamics speeds up the ejection, the dynamic characteristics are not changed. When bending rigidity is included in the polymer model, the capsid ejection enters a completely different dynamic regime. This shows as the cumulative waiting times scaling with the number of ejected beads when the persistence length of the polymer is sufficiently large compared to the capsid diameter.
Translated title of the contributionYksittäisen polymeerin dynamiikka ahtaissa geometrioissa: kapsidiejektio ja sedimentaatio
Original languageEnglish
QualificationDoctor's degree
Awarding Institution
  • Aalto University
  • Lampinen, Jouko, Supervising Professor
  • Linna, Riku, Thesis Advisor
Print ISBNs978-952-60-7715-4
Electronic ISBNs978-952-60-7716-1
Publication statusPublished - 2017
MoE publication typeG5 Doctoral dissertation (article)


  • polymers
  • molecular dynamics
  • capsid ejection
  • virus
  • sedimentation
  • knots

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