Hauptseminar Multiscale Simulations SS 2016/Ion transport through nanopores via atomistic simulations

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Topic: Ion transport through nanopores via atomistic simulations
Speaker: tba
Tutor: Florian Weik

Overview over nanopores and sensing applications.
DNA pore blockage experiments by Smeets. et. al. and relation to DNA sequencing
Infinite cylinder model and introduction of Poisson-Boltzmann (PB) theory and Stokes flow
Atomitic description of the system
- Force fields
- Model
- Results and comparison to PB theory.

Literature

C. Dekker.
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Nature Nanotech 2:209–215, 2007.
[PDF] (871 KB) [DOI]
Stefan Howorka, Zuzanna Siwy.
Nanopore analytics: sensing of single molecules.
Chemical Society Reviews 38(8):2360–2384, 2009.
[DOI]
B.M. Venkatesan, R. Bashir.
Nanopore sensors for nucleic acid analysis.
Nature Nanotechnology 6(10):615–624, 2011.
BN Miles, AP Ivanov, KA Wilson, F Dogan, D Japrung, JB Edel.
Single molecule sensing with solid-state nanopores: novel materials, methods, and applications.
Chemical Society Reviews 42:15–28, 2013.
[DOI]
Stefan Kesselheim, Wojciech Müller, Christian Holm.
Origin of Current Blockades in Nanopore Translocation Experiments.
Physical Review Letters 112(1):018101, 2014.
[PDF] (351 KB) [DOI]
Stefan Kesselheim.
Simulations of DNA Translocation through nanopores.
PhD thesis, Universitaet Stuttgart, 2014.
Ralph M. M. Smeets, Ulrich F. Keyser, Diego Krapf, Meng-Yue Wu, Nynke H. Dekker, Cees Dekker.
Salt dependence of ion transport and DNA translocation through solid-state nanopores.
Nano Letters 6:89–95, 2006.
[PDF] (993 KB)
Markus Deserno, Christian Holm, Jürgen Blaul, Matthias Ballauff, Matthias Rehahn.
The Osmotic Coefficient of Rod-like Polyelectrolytes: Computer Simulation, Analytical Theory, and Experiment.
European Physical Journal E 5:97–103, 2001.
[PDF] (147 KB) [DOI]