Translocation of Heterogeneous Polymers through a Nanopore

Translocation of Heterogeneous Polymers through a Nanopore

De Kever, M.C.A.

Dubbeldam, J.L.A. (mentor)

Electrical Engineering, Mathematics and Computer Science

Applied Mathematics

Mathematical Physics

2011-05-25

Translocating a chain of different beads through a very small pore can be used as a first step of modelling a DNA chain that passes through a nanopore. This translocation process offers a variety of possibilities in chemical and biological processes, for instance rapid DNA sequencing. In this thesis the chain is modelled as a polymer with different types of monomers as beads. The translocation dynamics of heterogeneous polymers through nanopores can be modelled using the LJ and FENE potentials and different interaction strengths between the monomers of the polymer and the pore. The translocation time gives important information of the chain sequence, depending on the length of the polymer. The waiting time is defined as the time a specific monomer stays inside the pore. This waiting time in particular gives useful results considering the chain sequence. Simulations reveal that the waiting time of the last monomer can define the type of monomer under consideration. Monomers with a high interaction with the pore will stay inside considerably longer. We found that from the average waiting time it is possible to retrieve the original sequence of the beads constituting the chain.

Translocation
Nanopores
Heterogeneous polymer
Sequencing
Translocation time
Waiting time
DNA

http://resolver.tudelft.nl/uuid:da94b28e-e056-496b-9649-78282d11ea6a

2011-05-25

Student theses

master thesis

(c) 2011 De Kever, M.C.A.