Difference between revisions of "DNA Electrophoresis"

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__NOTOC__
 
__NOTOC__
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[[Image::Elfse.png| ]]
 
[[Image:Elfse.png|300px|right|thumb|End labeled free-solution electrophoresis (ELFSE): Simulation snapshot]]
 
[[Image:Elfse.png|300px|right|thumb|End labeled free-solution electrophoresis (ELFSE): Simulation snapshot]]
  
'''Electrophoresis''' is one of the main techniques to separate DNA
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<onlyinclude>'''Electrophoresis''' is one of the main techniques to separate DNA molecules by size and has shown its effectiveness in the sequencing of entire genomes, including our own. This success story also increased the demand for improved and faster sequencing methods, in order to meet the upcoming challenges.</onlyinclude>
molecules by size and has shown its effectiveness in the sequencing of entire
 
genomes, including our own. This success story also increased the demand for improved and faster sequencing methods, in order to meet the upcoming challenges.  
 
  
Over the last years, many experimental investigations have been
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More recently, the DNA has been investigated as a material for the self assembly of complex three dimensional structures. These structures have been investigated in the scientific community as a material for drug delivery or nanomachines. However, even the fundamental understanding of the ion dynamics in electric field driven nanopore translocation of such structures is not fully understood yet. Such systems are therefore investigated via a multi-scale approach from all-atom models to mean-field models.
performed in the field of electrophoresis, in order to improve
 
existing methods or to develop new separation techniques which yield a
 
faster or better separation. These experimental
 
improvements gave rise to many interesting questions that still need to be dealt
 
with from a theoretical point of view.
 
 
 
The aim of this research is to provide these fundamental understandings
 
of the electrophoretic separation process by means of computer simulations using {{ES}}.  
 
  
 
Special topics that are currently under investigation are:
 
Special topics that are currently under investigation are:
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* end-labeled free-solution electrophoresis
 
* end-labeled free-solution electrophoresis
 
* electrophoresis in confined geometries
 
* electrophoresis in confined geometries
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* current modulation of DNA structures in a pore
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Hydrodynamic interactions are implemented in simulations by using a frictional coupling of the MD particles to a Lattice Boltzmann fluid. This efficient way of treating hydrodynamics enables a detailed study of the complex electrohydrodynamic interactions.
  
 
== Coworkers ==
 
== Coworkers ==
 
* [[Christian Holm]]: Project supervisor
 
* [[Christian Holm]]: Project supervisor
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* [[Kai Szuttor]]
 
* [[Kai Grass]]: PhD thesis on ''Hydrodynamic effects in polyelectrolyte electrophoresis''
 
* [[Kai Grass]]: PhD thesis on ''Hydrodynamic effects in polyelectrolyte electrophoresis''
  
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== Publications ==
 
== Publications ==
None so far.
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<bibentry pdflink="yes">szuttor21a</bibentry>
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<bibentry pdflink="yes">ahlrichs99a</bibentry>
  
 
== Links ==
 
== Links ==
 
* {{Download|MMSD07-poster.pdf|Poster presented at MMSD07}}
 
* {{Download|MMSD07-poster.pdf|Poster presented at MMSD07}}
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[[Category:Research]]

Latest revision as of 14:10, 13 May 2021


End labeled free-solution electrophoresis (ELFSE): Simulation snapshot

Electrophoresis is one of the main techniques to separate DNA molecules by size and has shown its effectiveness in the sequencing of entire genomes, including our own. This success story also increased the demand for improved and faster sequencing methods, in order to meet the upcoming challenges.

More recently, the DNA has been investigated as a material for the self assembly of complex three dimensional structures. These structures have been investigated in the scientific community as a material for drug delivery or nanomachines. However, even the fundamental understanding of the ion dynamics in electric field driven nanopore translocation of such structures is not fully understood yet. Such systems are therefore investigated via a multi-scale approach from all-atom models to mean-field models.

Special topics that are currently under investigation are:

  • free-solution electrophoresis
  • end-labeled free-solution electrophoresis
  • electrophoresis in confined geometries
  • current modulation of DNA structures in a pore

Hydrodynamic interactions are implemented in simulations by using a frictional coupling of the MD particles to a Lattice Boltzmann fluid. This efficient way of treating hydrodynamics enables a detailed study of the complex electrohydrodynamic interactions.

Coworkers

Collaborators

  • M. Hervé Cottet, CNRS laboratory, Université Montpellier 2, Montpellier, France
  • Ulrich Scheler, Leibnitz-Institute for Polymer Research (IPF), Dresden, Germany
  • Gary W. Slater, University of Ottawa, Ottawa, Canada

Publications


Links