Difference between revisions of "Jens Smiatek"
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Dr. Jens Smiatek
Postdoc
| Line 38: | Line 38: | ||
My profile at [http://scholar.google.de/citations?user=-RgaRekAAAAJ "Scholar Google"] | My profile at [http://scholar.google.de/citations?user=-RgaRekAAAAJ "Scholar Google"] | ||
| − | * Hickey, O. A.; Holm, C.; Smiatek, J.: Lattice-Boltzmann simulations of the electrophoretic stretching of polyelectrolytes - the importance of hydrodynamic interactions, submitted (2014) | + | * Hickey, O. A.; Holm, C.; Smiatek, J. |
| + | *: Lattice-Boltzmann simulations of the electrophoretic stretching of polyelectrolytes - the importance of hydrodynamic interactions, submitted (2014) | ||
| − | * Smiatek, J.; Heuer, A.: Deprotonation mechanism of a single-stranded DNA i-motif, submitted (2014) | + | * Smiatek, J.; Heuer, A. |
| + | *: Deprotonation mechanism of a single-stranded DNA i-motif, submitted (2014) | ||
| − | * Bohner, M. U.; Zemann, J.; Smiatek, J.; Arnold, A.; Kästner, J.: Nudged-elastic band used to find reaction coordinates based on the free energy, ''J. Chem. Phys.'' '''140''', 074109 (2014) | + | * Bohner, M. U.; Zemann, J.; Smiatek, J.; Arnold, A.; Kästner, J. |
| + | *: Nudged-elastic band used to find reaction coordinates based on the free energy, ''J. Chem. Phys.'' '''140''', 074109 (2014) | ||
| − | * Smiatek, J.; Wohlfarth, A. and Holm, C.: The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents - a computational study, ''New J. Phys.'' '''16''', 025001 (2014) | + | * Smiatek, J.; Wohlfarth, A. and Holm, C. |
| + | *: The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents - a computational study, ''New J. Phys.'' '''16''', 025001 (2014) | ||
| − | * Smiatek, J.: Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres, ''J. Phys. Chem. B.'' '''118''', 771 (2014) | + | * Smiatek, J. |
| + | *: Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres, ''J. Phys. Chem. B.'' '''118''', 771 (2014) | ||
| − | * Smiatek, J.; Janssen-Mueller, D.; Friedrich, R. and Heuer, A.: Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand, ''Physica A'' '''394''', 136 (2014) | + | * Smiatek, J.; Janssen-Mueller, D.; Friedrich, R. and Heuer, A. |
| + | *: Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand, ''Physica A'' '''394''', 136 (2014) | ||
| − | * Smiatek, J.; Harishchandra, R. K.; Galla, H.-J. and Heuer, A.: Low concentrated hydroxyectoine solutions in presence of DPPC lipid bilayers: a computer simulation study, ''Biophys. Chem.'' '''180–181''', 102 (2013) | + | * Smiatek, J.; Harishchandra, R. K.; Galla, H.-J. and Heuer, A. |
| + | *: Low concentrated hydroxyectoine solutions in presence of DPPC lipid bilayers: a computer simulation study, ''Biophys. Chem.'' '''180–181''', 102 (2013) | ||
| − | * Hentschel, C.; Wagner, H.; Smiatek, J.; Heuer, A.; Fuchs, H.; Zhang, X.; Studer, A. and Chi, L.: AFM-based force spectroscopy on polystyrene brushes: Effect of brush thickness on protein adsorption, '' Langmuir'' '''29''', 1850 (2013) | + | * Hentschel, C.; Wagner, H.; Smiatek, J.; Heuer, A.; Fuchs, H.; Zhang, X.; Studer, A. and Chi, L. |
| + | *: AFM-based force spectroscopy on polystyrene brushes: Effect of brush thickness on protein adsorption, '' Langmuir'' '''29''', 1850 (2013) | ||
| − | * Smiatek, J.; Wagner, H.; Hentschel C.; Chi, L.; Studer, A. and Heuer, A.: Coat thickness dependent adsorption of hydrophobic molecules at polymer brushes, ''J. Chem. Phys.'' '''138''', 044904 (2013) | + | * Smiatek, J.; Wagner, H.; Hentschel C.; Chi, L.; Studer, A. and Heuer, A. |
| + | *: Coat thickness dependent adsorption of hydrophobic molecules at polymer brushes, ''J. Chem. Phys.'' '''138''', 044904 (2013) | ||
| − | * Smiatek, J.; Liu, D. and Heuer, A.: Unfolding pathways and the free energy landscape of a single-stranded DNA i-motif, ''From Computational Biophysics to Systems Biology (CBSB11)'', IAS Series '''8''', 201 (2012) | + | * Smiatek, J.; Liu, D. and Heuer, A. |
| + | *: Unfolding pathways and the free energy landscape of a single-stranded DNA i-motif, ''From Computational Biophysics to Systems Biology (CBSB11)'', IAS Series '''8''', 201 (2012) | ||
| − | * Meinhardt, S.; Smiatek, J.; Eichhorn, R. and Schmid, F.: Separation of chiral particles in micro- or nanofluidic channels, ''Phys. Rev. Lett.'' '''108''', 214504 (2012) | + | * Meinhardt, S.; Smiatek, J.; Eichhorn, R. and Schmid, F. |
| + | *: Separation of chiral particles in micro- or nanofluidic channels, ''Phys. Rev. Lett.'' '''108''', 214504 (2012) | ||
| − | * Smiatek, J.; Harishchandra, R. K.; Rubner, O.; Galla, H.-J. and Heuer A.: Properties of compatible solutes in aqueous solution, ''Biophys. Chem.'' '''160''', 62 (2012) | + | * Smiatek, J.; Harishchandra, R. K.; Rubner, O.; Galla, H.-J. and Heuer A. |
| + | *: Properties of compatible solutes in aqueous solution, ''Biophys. Chem.'' '''160''', 62 (2012) | ||
| − | * Smiatek, J. and Schmid, F.: [http://cdn.intechopen.com/pdfs/29685/InTech-Mesoscopic_simulation_methods_for_studying_flow_and_transport_in_electric_fields_in_micro_and_nanochannels.pdf Mesoscopic simulation methods for studying flow and transport in electric fields in micro- and nanochannels], invited chapter for ''Advances in Microfluidics'', edited by Ryan T. Kelly, InTech, Rijeka (2012) | + | * Smiatek, J. and Schmid, F.: |
| + | *: [http://cdn.intechopen.com/pdfs/29685/InTech-Mesoscopic_simulation_methods_for_studying_flow_and_transport_in_electric_fields_in_micro_and_nanochannels.pdf Mesoscopic simulation methods for studying flow and transport in electric fields in micro- and nanochannels], invited chapter for ''Advances in Microfluidics'', edited by Ryan T. Kelly, InTech, Rijeka (2012) | ||
| − | * Smiatek, J.; Liu, D. and Heuer, A.: High temperature unfolding simulations of a single-stranded DNA i-motif, ''Curr. Phys. Chem.'' '''2''', 115 (2012) | + | * Smiatek, J.; Liu, D. and Heuer, A. |
| + | *: High temperature unfolding simulations of a single-stranded DNA i-motif, ''Curr. Phys. Chem.'' '''2''', 115 (2012) | ||
| − | * Smiatek, J.; Chen, C.; Liu, D. and Heuer, A.: Stable conformations of a single-stranded deprotonated DNA i-motif, ''J. Phys. Chem. B'' '''115''', 13788 (2011) | + | * Smiatek, J.; Chen, C.; Liu, D. and Heuer, A. |
| + | *: Stable conformations of a single-stranded deprotonated DNA i-motif, ''J. Phys. Chem. B'' '''115''', 13788 (2011) | ||
| − | * Smiatek, J. and Schmid, F.: Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels, ''Comp. Phys. Comm.'' '''182''', 1941 (2011) | + | * Smiatek, J. and Schmid, F. |
| + | *: Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels, ''Comp. Phys. Comm.'' '''182''', 1941 (2011) | ||
| − | * Smiatek, J. and Heuer, A.: Calculation of free energy landscapes: a histogram reweighted metadynamics approach, ''J. Comp. Chem.'' '''32''', 2084 (2011) | + | * Smiatek, J. and Heuer, A. |
| + | *: Calculation of free energy landscapes: a histogram reweighted metadynamics approach, ''J. Comp. Chem.'' '''32''', 2084 (2011) | ||
| − | * Smiatek, J. and Schmid F.: Mesoscopic simulations of polyelectrolyte electrophoresis in nanochannels in ''High Performance Computing in Science and Engineering '10''; Springer, Heidelberg (2011) | + | * Smiatek, J. and Schmid F. |
| + | *: Mesoscopic simulations of polyelectrolyte electrophoresis in nanochannels in ''High Performance Computing in Science and Engineering '10''; Springer, Heidelberg (2011) | ||
| − | * Smiatek, J. and Schmid, F.: Polyelectrolyte electrophoresis in nanochannels: a Dissipative Particle Dynamics simulation, ''J. Phys. Chem. B'' '''114''', 6266 (2010) | + | * Smiatek, J. and Schmid, F. |
| + | *: Polyelectrolyte electrophoresis in nanochannels: a Dissipative Particle Dynamics simulation, ''J. Phys. Chem. B'' '''114''', 6266 (2010) | ||
| − | * Smiatek, J.; Sega, M.; Schiller, U. D.; Holm, C. and Schmid, F.: Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study, ''J. Chem. Phys.'' '''130''', 244702 (2009) | + | * Smiatek, J.; Sega, M.; Schiller, U. D.; Holm, C. and Schmid, F. |
| + | *: Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study, ''J. Chem. Phys.'' '''130''', 244702 (2009) | ||
| − | * Smiatek J.: [http://bieson.ub.uni-bielefeld.de/volltexte/2009/1475/pdf/Diss.pdf ''Mesoscopic simulations of electrohydrodynamic phenomena''], PhD thesis, Bielefeld University, Germany (2009) | + | * Smiatek J. |
| + | *: [http://bieson.ub.uni-bielefeld.de/volltexte/2009/1475/pdf/Diss.pdf ''Mesoscopic simulations of electrohydrodynamic phenomena''], PhD thesis, Bielefeld University, Germany (2009) | ||
| − | * Smiatek, J.; Allen, M. P. and Schmid, F.: Tunable-slip boundaries for coarse-grained simulations of fluid flow, ''Europ. Phys. J. E'' '''26''', 115 (2008) | + | * Smiatek, J.; Allen, M. P. and Schmid, F. |
| + | *: Tunable-slip boundaries for coarse-grained simulations of fluid flow, ''Europ. Phys. J. E'' '''26''', 115 (2008) | ||
== Multimedia == | == Multimedia == | ||
* '''High temperature unfolding dynamics of a single-stranded deprotonated DNA i-motif''' | * '''High temperature unfolding dynamics of a single-stranded deprotonated DNA i-motif''' | ||
{{#widget:YouTube|id=PLgswwOen1Q|width=670|height=500}} | {{#widget:YouTube|id=PLgswwOen1Q|width=670|height=500}} | ||
Revision as of 20:14, 20 February 2014
Postdoc
| Office: | 1.032 |
|---|---|
| Phone: | +49 711 685-63757 |
| Fax: | +49 711 685-63658 |
| Email: | smiatek _at_ icp.uni-stuttgart.de |
| Address: | Dr. Jens Smiatek Institute for Computational Physics Universität Stuttgart Allmandring 3 70569 Stuttgart Germany |
Research interests
- Specific DNA structures: i-motif and g-quadruplex
- Protein folding
- Hydrophobic hydration
- Free energy landscapes
- Influence of solvent properties on structure formation (solvent-solute interactions)
- Influence of osmolytes on water structure
- Electrohydrodynamics
- Polyelectrolytes and interactions with ions
- Microscale flows
- Method development
Publications
My profile at "Scholar Google"
- Hickey, O. A.; Holm, C.; Smiatek, J.
- Lattice-Boltzmann simulations of the electrophoretic stretching of polyelectrolytes - the importance of hydrodynamic interactions, submitted (2014)
- Smiatek, J.; Heuer, A.
- Deprotonation mechanism of a single-stranded DNA i-motif, submitted (2014)
- Bohner, M. U.; Zemann, J.; Smiatek, J.; Arnold, A.; Kästner, J.
- Nudged-elastic band used to find reaction coordinates based on the free energy, J. Chem. Phys. 140, 074109 (2014)
- Smiatek, J.; Wohlfarth, A. and Holm, C.
- The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents - a computational study, New J. Phys. 16, 025001 (2014)
- Smiatek, J.
- Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres, J. Phys. Chem. B. 118, 771 (2014)
- Smiatek, J.; Janssen-Mueller, D.; Friedrich, R. and Heuer, A.
- Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand, Physica A 394, 136 (2014)
- Smiatek, J.; Harishchandra, R. K.; Galla, H.-J. and Heuer, A.
- Low concentrated hydroxyectoine solutions in presence of DPPC lipid bilayers: a computer simulation study, Biophys. Chem. 180–181, 102 (2013)
- Hentschel, C.; Wagner, H.; Smiatek, J.; Heuer, A.; Fuchs, H.; Zhang, X.; Studer, A. and Chi, L.
- AFM-based force spectroscopy on polystyrene brushes: Effect of brush thickness on protein adsorption, Langmuir 29, 1850 (2013)
- Smiatek, J.; Wagner, H.; Hentschel C.; Chi, L.; Studer, A. and Heuer, A.
- Coat thickness dependent adsorption of hydrophobic molecules at polymer brushes, J. Chem. Phys. 138, 044904 (2013)
- Smiatek, J.; Liu, D. and Heuer, A.
- Unfolding pathways and the free energy landscape of a single-stranded DNA i-motif, From Computational Biophysics to Systems Biology (CBSB11), IAS Series 8, 201 (2012)
- Meinhardt, S.; Smiatek, J.; Eichhorn, R. and Schmid, F.
- Separation of chiral particles in micro- or nanofluidic channels, Phys. Rev. Lett. 108, 214504 (2012)
- Smiatek, J.; Harishchandra, R. K.; Rubner, O.; Galla, H.-J. and Heuer A.
- Properties of compatible solutes in aqueous solution, Biophys. Chem. 160, 62 (2012)
- Smiatek, J. and Schmid, F.:
- Mesoscopic simulation methods for studying flow and transport in electric fields in micro- and nanochannels, invited chapter for Advances in Microfluidics, edited by Ryan T. Kelly, InTech, Rijeka (2012)
- Smiatek, J.; Liu, D. and Heuer, A.
- High temperature unfolding simulations of a single-stranded DNA i-motif, Curr. Phys. Chem. 2, 115 (2012)
- Smiatek, J.; Chen, C.; Liu, D. and Heuer, A.
- Stable conformations of a single-stranded deprotonated DNA i-motif, J. Phys. Chem. B 115, 13788 (2011)
- Smiatek, J. and Schmid, F.
- Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels, Comp. Phys. Comm. 182, 1941 (2011)
- Smiatek, J. and Heuer, A.
- Calculation of free energy landscapes: a histogram reweighted metadynamics approach, J. Comp. Chem. 32, 2084 (2011)
- Smiatek, J. and Schmid F.
- Mesoscopic simulations of polyelectrolyte electrophoresis in nanochannels in High Performance Computing in Science and Engineering '10; Springer, Heidelberg (2011)
- Smiatek, J. and Schmid, F.
- Polyelectrolyte electrophoresis in nanochannels: a Dissipative Particle Dynamics simulation, J. Phys. Chem. B 114, 6266 (2010)
- Smiatek, J.; Sega, M.; Schiller, U. D.; Holm, C. and Schmid, F.
- Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study, J. Chem. Phys. 130, 244702 (2009)
- Smiatek J.
- Mesoscopic simulations of electrohydrodynamic phenomena, PhD thesis, Bielefeld University, Germany (2009)
- Smiatek, J.; Allen, M. P. and Schmid, F.
- Tunable-slip boundaries for coarse-grained simulations of fluid flow, Europ. Phys. J. E 26, 115 (2008)
Multimedia
- High temperature unfolding dynamics of a single-stranded deprotonated DNA i-motif