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.
"Solid-state nanopores".
Nature Nanotech 2(209–215), 2007.
[PDF] (871 KB) [DOI]
Howorka, Stefan and Siwy, Zuzanna.
"Nanopore analytics: sensing of single molecules".
Chemical Society Reviews 38(8)(2360–2384), 2009.
[DOI]
Venkatesan, B.M. and Bashir, R..
"Nanopore sensors for nucleic acid analysis".
Nature Nanotechnology 6(10)(615–624), 2011.
Miles, BN and Ivanov, AP and Wilson, KA and Dogan, F and Japrung, D and Edel, JB.
"Single molecule sensing with solid-state nanopores: novel materials, methods, and applications".
Chemical Society Reviews 42(15–28), 2013.
[DOI]
Kesselheim, Stefan and Müller, Wojciech and Holm, Christian.
"Origin of Current Blockades in Nanopore Translocation Experiments".
Physical Review Letters 112(018101), 2014.
[PDF] (351 KB) [DOI]
Stefan Kesselheim.
"Simulations of DNA Translocation through nanopores".
PhD thesis, Universitaet Stuttgart, 2014.
Ralph M. M. Smeets and Ulrich F. Keyser and Diego Krapf and Meng-Yue Wu and Nynke H. Dekker and 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 and Christian Holm and Jürgen Blaul and Matthias Ballauff and 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]