Jens Smiatek

Dr. Jens Smiatek
Group leader

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

Lectures - Material

Simulationsmethoden fuer Master-Studierende B (SS 2015)

• Worksheet 1 (zip-File with input files for GROMACS) Diffusion processes and properties of atomistic water models
  • Worksheet 1 (work sheet as a single PDF file)
  • GROMACS Download
  • How to visualize GROMACS trajectories with VMD

Publications

My profile at "Scholar Google"

• Volker Lesch, Andreas Heuer, Christian Holm, Jens Smiatek.
  Solvent effects of 1-ethyl-3-methylimidazolium acetate: solvation and dynamic behavior of polar and apolar solutes.
  Physical Chemistry Chemical Physics 17(13):8480–8490, 2015.
  [PDF] (2.7 MB) [DOI]
• Andreas Wohlfarth, Jens Smiatek, Klaus-Dieter Kreuer, Shogo Takamuku, Patric Jannasch, Joachim Maier.
  Proton Dissociation of Sulfonated Polysulfones: Influence of Molecular Structure and Conformation.
  Macromolecules 48(4):1134–1143, 2015.
  [PDF] (1.5 MB) [DOI]
• Jiajia Zhou, Jens Smiatek, Evgeny S Asmolov, Olga I Vinogradova, Friederike Schmid.
  Application of Tunable-Slip Boundary Conditions in Particle-Based Simulations.
  In High Performance Computing in Science and Engineering '14.
  Springer, 2014.
  
• Andreas Heuer, Jens Smiatek, Bernd Strauss, Dennis Riedl.
  Informationsgehalt von Fussball-Spieldaten.
  In Fussball in Forschung und Lehre - Beiträge und Analysen zum Fusballsport XIX. Part of Schriften der Deutschen Vereinigung für Sportwissenschaft Band 240.
  Czwalina, 2014.
  
• Anand Narayanan Krishnamoorthy, Christian Holm, Jens Smiatek.
  Local Water Dynamics around Antifreeze Protein Residues in the Presence of Osmolytes: The Importance of Hydroxyl and Disaccharide Groups.
  The Journal of Physical Chemistry B 118(40):11613–11621, 2014.
  [PDF] (1.0 MB) [DOI]
• Samantha Micciulla, Pedro A. Sánchez, Jens Smiatek, Baofu Qiao, Marcello Sega, André Laschewsky, Christian Holm, Regine von Klitzing.
  Layer-by-Layer Formation of Oligoelectrolyte Multilayers: A Combined Experimental and Computational Study.
  Soft Materials 12(sup1):S14–S21, 2014.
  [PDF] (581 KB) [DOI]
• Owen A. Hickey, Christian Holm, Jens Smiatek.
  Lattice-Boltzmann simulations of the electrophoretic stretching of polyelectrolytes: The importance of hydrodynamic interactions.
  The Journal of Chemical Physics 140(16):164904, 2014.
  [PDF] (739 KB) [DOI]
• Jens Smiatek, Andreas Heuer.
  Deprotonation mechanism of a single-stranded DNA i-motif.
  RSC Advances 4(33):17110–17113, 2014.
  [PDF] (380 KB) [DOI]
• Matthias U. Bohner, Johannes Zeman, Jens Smiatek, Axel Arnold, Johannes Kästner.
  Nudged-elastic band used to find reaction coordinates based on the free energy.
  The Journal of Chemical Physics 140(7):074109, 2014.
  [PDF] (637 KB) [DOI]
• Jens Smiatek, Andreas Wohlfarth, Christian Holm.
  The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents—a computational study.
  New Journal of Physics 16(2):025001, 2014.
  [PDF] (742 KB) [DOI]
• Jens Smiatek.
  Osmolyte Effects: Impact on the Aqueous Solution around Charged and Neutral Spheres.
  The Journal of Physical Chemistry B 118(3):771–782, 2014.
  [PDF] (1.7 MB) [DOI]
• Jens Smiatek, Daniel Janssen-Müller, Rudolf Friedrich, Andreas Heuer.
  Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand.
  Physica A: Statistical Mechanics and its Applications 394(0):136–144, 2014.
  [PDF] (930 KB) [DOI] [URL]
• J. Smiatek, R. K. Harishchandra, H.-J. Galla, A. Heuer.
  Low Concentrated Hydroxiectoine Solutions in Presence of DPPC Lipid Bilayers: A Computer Simulation Study.
  Biophysical Chemistry 180:102–109, 2013.
  [PDF] (895 KB) [DOI]
• Jens Smiatek, Andreas Heuer, Hendrik Wagner, Armido Studer, Carsten Hentschel, Lifeng Chi.
  Coat thickness dependent adsorption of hydrophobic molecules at polymer brushes.
  The Journal of Chemical Physics 138(4), 2013.
  [PDF] (759 KB) [DOI]
• Carsten Hentschel, Hendrik Wagner, Jens Smiatek, Andreas Heuer, Harald Fuchs, Xi Zhang, Armido Studer, Lifeng Chi.
  AFM-based Force Spectroscopy on Polystyrene Brushes: Effect of Brush Thickness on Protein Adsorption.
  Langmuir 29:1850–1856, 2013.
  
• Jens Smiatek, Dongsheng Liu, Andreas Heuer.
  Unfolding pathways and the free energy landscape of a single-stranded DNA i-motif.
  In From Computational Biophysics to Systems Biology (CBSB11). Part of IAS-Series.
  NIC-Publishing, 2012.
  
• Sebastian Meinhardt, Jens Smiatek, Ralf Eichhorn, Friederike Schmid.
  Separation of Chiral Particles in Micro- or Nanofluidic Channels.
  Physical Review Letters 108(21):214504, 2012.
  [PDF] (493 KB) [DOI]
• Jens Smiatek, Rakesh Kumar Harishchandra, Oliver Rubner, Hans-Joachim Galla, Andreas Heuer.
  Properties of compatible solutes in aqueous solution.
  Biophysical Chemistry 160(1):62–68, 2012.
  [PDF] (856 KB) [DOI]
• Jens Smiatek, Friederike Schmid.
  Mesoscopic Simulation Methods for Studying Flow and Transport in Electric Fields in Micro- and Nanochannels.
  In Advances in Microfluidics, chapter 5. Edited by Ryan T. Kelly.
  InTech, 2012.
  [PDF] (427 KB) [DOI] [URL]
• Jens Smiatek, Dongsheng Liu, Andreas Heuer.
  High temperature unfolding simulations of a single-stranded DNA i-motif.
  Current Physical Chemistry 2:115–123, 2012.
  
• Jens Smiatek, Chun Chen, Dongsheng Liu, Andreas Heuer.
  Stable Conformations of a Single Stranded Deprotonated DNA i-Motif.
  Journal of Physical Chemistry B 115(46):13788–13795, 2011.
  [PDF] (4.7 MB) [DOI]
• Jens Smiatek, Friederike Schmid.
  Mesoscopic Simulations of Polyelectrolyte Electrophoresis in Nanochannels.
  In High Performance Computing in Science and Engineering '10, pages 53–67. Edited by Wolfgang E. Nagel, Dietmar B. Kröner, Michael M. Resch.
  Springer Berlin Heidelberg, 2011. ISBN: 978-3-642-15747-9.
  [DOI]
• Jens Smiatek, Andreas Heuer.
  Calculation of free energy landscapes: A histogram reweighted metadynamics approach.
  Journal of Computational Chemistry 32(10):2084–2096, 2011.
  [PDF] (595 KB) [DOI]
• Jens Smiatek, Friederike Schmid.
  Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels.
  Computer Physics Communications 182(9):1941–1944, 2011.
  [PDF] (277 KB) [DOI] [URL]
• Jens Smiatek, Friederike Schmid.
  Polyelectrolyte Electrophoresis in Nanochannels: A Dissipative Particle Dynamics Simulation.
  Journal of Physical Chemistry B 114(19):6266–6272, 2010.
  [PDF] (250 KB) [DOI]
• Jens Smiatek.
  Mesoscopic simulations of electrohydrodynamic phenomena.
  PhD thesis, Bielefeld University, Germany, jan, 2009.
  [PDF] (1.9 MB)
• Jens Smiatek, Marcello Sega, Christian Holm, Ulf D. Schiller, Friederike Schmid.
  Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study.
  The Journal of Chemical Physics 130(244702), 2009.
  [PDF] (370 KB) [DOI]
• Jens Smiatek, Michael P. Allen, Friederike Schmid.
  Tunable-slip boundaries for coarse-grained simulations of fluid flow.
  European Physical Journal E 26:115–122, 2008.
  [PDF] (179 KB)

Submitted Manuscripts

• Vögele, M.; Holm, C.; Smiatek, J.

  Properties of the Polarizable MARTINI Water Model: A Comparative Study for Aqueous Electrolyte Solutions, submitted (2015)

• Smiatek, J.; Riedl, D.; Heuer, A.

  Statistical properties of soccer, basketball and handball - A quantitative comparison, submitted (2015)

• Vögele, M.; Holm, C.; Smiatek, J.

  Coarse-Grained Simulations of Polyelectrolyte Complexes: MARTINI Based Models for Poly(styrene sulfonate) and Poly(diallyldimethylammonium), submitted (2015)

• Smiatek, J.

  Two sides of one coin - High and low concentrated aqueous urea solutions around differently charged spheres, submitted (2015)

Multimedia

• High temperature unfolding dynamics of a single-stranded deprotonated DNA i-motif