Hauptseminar Multiscale Simulations SS 2016/A coarse grained model for electrokinetic applications of DNA transport through nanopores
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- A coarse grained model for electrokinetic applications of DNA transport through nanopores
- Gary Davies
This topic deals with a simulation model of DNA transport through nanopores, based on the work of a previous MSc student here at the ICP. You will first understand the various components of the model, before understanding the simulation results of the model itself.
The key feature of the model is that water is no longer explicitly simulated, and instead we use a lattice Boltzmann model to solve the equations of motion of the fluid. The lattice Boltzmann method solves the Navier-Stokes equations, which are a set of continuum equations governing the motion of fluids.
You will discuss briefly the ideas behind the derivation of the Navier-Stokes equation, in order to appreciate its continuum nature. You must then discuss how the dynamics of the fluid are coupled to the charged particles that make up the DNA molecule in the simulations. You should talk about the thermalisation inherent in the model and the comparison of previous simulation results to theoretical expressions and experimental data.
The DNA model itself should be discussed. This will include a discussion of how to impose bond-angles between the charged particles and how to match the persistence length.
Finally, you will discuss the results of the simulations carried out in Tobias Rau's thesis on the eletrophoresis of DNA base pairs, and how the mobility of the DNA base pairs change.
G. Davies PhD thesis: "Modelling Colloidal Particles Adsorbed at Fluid-Fluid Interfaces" (2015) Chapter 3 Pages 51-65:
Tobias Rau Master's Thesis "A Realistic DNA Model for Electrokinetic Applications" (2015).
B. Dünweg and A. J. C. Ladd "Lattice Boltzmann Simulations of Soft Matter Systems"
Advanced Computer Simulation Approaches for Soft Matter Sciences III Volume 221 of the series Advances in Polymer Science pp 89-166