Jens Smiatek

From ICPWiki
Revision as of 06:39, 8 December 2017 by Smiatek (talk | contribs)
Jump to: navigation, search
Smiatek DNA1.jpg
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

  • Biomolecules and specific DNA structures: i-motif and g-quadruplex
  • Solvent effects
  • Free energy landscapes
  • Solvent-solute interactions
  • Osmolytes and co-solutes
  • Electrohydrodynamics
  • Polyelectrolytes and interactions with ions
  • Microscale flows
  • Method development

Curriculum Vitae

A detailed CV can be found here.

Publications

My profile at "Scholar Google"

  • Markthaler, D.; Zeman, J.; Baz, J.; Smiatek, J.; Hansen, N.
Validation of Trimethylamine-N-Oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions.
J. Phys. Chem. B 121 (10674-10688), 2017.
DOI: 10.1021/acs.jpcb.7b07774 (2017)
  • Belyanchikov, M. A.; Zhukov, E. S.; Tertia, S.; Zhugayevych, A.; Dressel, M.; Uhlig, F.; Smiatek, J.; Fyta, M.; Thomas, V. G.; Gorshunov, B. P.
Vibrational states of nano-confined water molecules in beryl based on first principles calculations and optical experiments.
Phys. Chem. Chem. Phys. 19 (30740-30748), 2017.
DOI: 10.1039/C7CP06472A
    • Johannes Zeman and Frank Uhlig and Jens Smiatek and Christian Holm.
      "A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate".
      Journal of Physics: Condensed Matter 29(50)(504004), 2017.
      [PDF] (2 MB) [DOI]
    • Uhlig, Frank and Smiatek, Jens and Holm, Christian.
      "Many-body effects in simulations of ionic liquids".
      In Proceedings of the 3rd bwHPC-Symposium, Heidelberg 2016, pages 121–123.
      heiBOOKS, 2017.
      [PDF] (2 MB) [DOI]
    • Tamal Roy and Kai Szuttor and Jens Smiatek and Christian Holm and Steffen Hardt.
      "Electric-field-induced stretching of surface-tethered polyelectrolytes in a microchannel".
      Physical Review E 96(3)(032503), 2017.
      [PDF] (794 KB) [DOI]
    • Niskanen, Johannes and Sahle, Christoph J. and Gilmore, Keith and Uhlig, Frank and Smiatek, Jens and Föhlisch, Alexander.
      "Disentangling structural information from core-level excitation spectra".
      Physical Review E 96(013319), 2017.
      [PDF] (2 MB) [DOI] [URL]
    • Roy, Tamal and Szuttor, Kai and Smiatek, Jens and Holm, Christian and Hardt, Steffen.
      "Stretching of surface-tethered polymers in pressure-driven flow under confinement".
      Soft Matter 13(6189–6196), 2017.
      [PDF] (3 MB) [DOI]
    • Kobayashi, Takeshi and Reid, Joshua and Shimizu, Seishi and Fyta, Maria and Smiatek, Jens.
      "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood-Buff approaches".
      Physical Chemistry Chemical Physics 19(18924–18937), 2017.
      [PDF] (5 MB) [DOI]
    • Diddens, Diddo and Lesch, Volker and Heuer, Andreas and Smiatek, Jens.
      "Aqueous Ionic Liquids and Their Influence on Peptide Conformations: Denaturation and Dehydration Mechanisms".
      Physical Chemistry Chemical Physics 19(20430–20440), 2017.
      [PDF] (4 MB) [DOI]
    • Kai Szuttor and Tamal Roy and Steffen Hardt and Christian Holm and Jens Smiatek.
      "The stretching force on a tethered polymer in pressure-driven flow".
      The Journal of Chemical Physics 147(3)(034902), 2017.
      [PDF] (1005 KB) [DOI]
    • Jens Smiatek.
      "Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results".
      Journal of Physics: Condensed Matter 29(23)(233001), 2017.
      [PDF] (2 MB) [DOI]
    • Landsgesell, Jonas and Holm, Christian and Smiatek, Jens.
      "Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method".
      The European Physical Journal Special Topics 226(725–736), 2017.
      [PDF] (287 KB) [DOI]
    • Landsgesell, Jonas and Holm, Christian and Smiatek, Jens.
      "Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions".
      Journal of Chemical Theory and Computation 13(2)(852–862), 2017.
      [PDF] (3 MB) [DOI]
    • Julian Michalowsky and Lars V. Schäfer and Christian Holm and Jens Smiatek.
      "A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions".
      The Journal of Chemical Physics 146(5)(054501), 2017.
      [PDF] (512 KB) [DOI]
    • Smiatek, Jens and Hansen, Niels and Kästner, Johannes.
      "Free Energy Calculation Methods and Rare Event Sampling Techniques for Biomolecular Simulations".
      In Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, pages 185–214.
      The Royal Society of Chemistry, 2017.
      [DOI] [URL]
    • Schroer, Martin A. and Michalowsky, Julian and Fischer, Birgit and Smiatek, Jens and Grübel, Gerhard.
      "Stabilizing Effect of TMAO on Globular PNIPAM States: Preferential Attraction Induces Preferential Hydration".
      Physical Chemistry Chemical Physics 18(31459–31470), 2016.
      [PDF] (3 MB) [DOI]
    • Krishnamoorthy, Anand Narayanan and Zeman, Johannes and Holm, Christian and Smiatek, Jens.
      "Preferential solvation and ion association properties in aqueous dimethyl sulfoxide solutions".
      Physical Chemistry Chemical Physics 18(31312–31322), 2016.
      [PDF] (4 MB) [DOI]
    • Lesch, Volker and Heuer, Andreas and Rad, Babak R. and Winter, Martin and Smiatek, Jens.
      "Atomistic insights into deep eutectic electrolytes: the influence of urea on the electrolyte salt LiTFSI in view of electrochemical applications".
      Physical Chemistry Chemical Physics 18(28403–28408), 2016.
      [PDF] (3 MB) [DOI] [URL]
    • Hahn, Marc Benjamin and Uhlig, Frank and Solomun, Tihomir and Smiatek, Jens and Sturm, Heinz.
      "Combined influence of ectoine and salt: spectroscopic and numerical evidence for compensating effects on aqueous solutions".
      Physical Chemistry Chemical Physics 18(41)(28398–28402), 2016.
      [PDF] (3 MB) [DOI]
    • Breitsprecher, Konrad and Krishnamoorthy, Anand Narayanan and Smiatek, Jens and Holm, Christian.
      "Force Field Optimization for Ionic Liquids: FFOIL".
      In High Performance Computing in Science and Engineering '15, pages 101–117.
      Springer, 2016.
      [PDF] (2 MB) [DOI]
    • Sánchez, Pedro A. and Smiatek, Jens and Qiao Baofu and Sega, Marcello and Holm, Christian.
      "Atomistic Simulation of Oligoelectrolyte Multilayers Growth".
      In High Performance Computing in Science and Engineering '15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015, pages 215–228. Editors: Nagel, E. Wolfgang and Kröner, H. Dietmar and Resch, M. Michael,
      Springer International Publishing, 2016.
      [PDF] (292 KB) [DOI]
    • Micciulla, Samantha and Michalowsky, Julian and Schroer, Martin A. and Holm, Christian and von Klitzing, Regine and Smiatek, Jens.
      "Concentration dependent effects of urea binding to poly(N-isopropylacrylamide) brushes: a combined experimental and numerical study".
      Physical Chemistry Chemical Physics 18(5324–5335), 2016.
      [PDF] (3 MB) [DOI]
    • Lesch, Volker and Heuer, Andreas and Holm, Christian and Smiatek, Jens.
      "Properties of Apolar Solutes in Alkyl Imidazolium-Based Ionic Liquids: The Importance of Local Interactions".
      ChemPhysChem 17(3)(387–394), 2016.
      [PDF] (2 MB) [DOI] [URL]
    • Vögele, Martin and Holm, Christian and Smiatek, Jens.
      "Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)".
      The Journal of Chemical Physics 143(24)(243151), 2015.
      [PDF] (910 KB) [DOI]
    • Marc Benjamin Hahn and Tihomir Solomun and Robert Wellhausen and Sabrina Hermann and Harald Seitz and Susann Meyer and Hans-Jörg Kunte and Johannes Zeman and Frank Uhlig and Jens Smiatek and Heinz Sturm.
      "Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA".
      The Journal of Physical Chemistry B 119(49)(15212–15220), 2015.
      [PDF] (479 KB) [DOI]
    • Fahrenberger, Florian and Hickey, Owen A. and Smiatek, Jens and Holm, Christian.
      "The influence of charged-induced variations in the local permittivity on the static and dynamic properties of polyelectrolyte solutions".
      The Journal of Chemical Physics 143(24)(243140), 2015.
      [PDF] (2 MB) [DOI]
    • Lesch, Volker and Heuer, Andreas and Tatsis, Vasileios A. and Holm, Christian and Smiatek, Jens.
      "Peptides in the presence of aqueous ionic liquids: tunable co-solutes as denaturants or protectants?".
      Physical Chemistry Chemical Physics 17(39)(26049–26053), 2015.
      [PDF] (2 MB) [DOI]
    • Fahrenberger, Florian and Hickey, Owen A. and Smiatek, Jens and Holm, Christian.
      "Importance of varying permittivity on the conductivity of polyelectrolyte solutions".
      Physical Review Letters 115(118301), 2015.
      [PDF] (523 KB) [DOI] [URL]
    • Vögele, Martin and Holm, Christian and Smiatek, Jens.
      "Properties of the polarizable MARTINI water model: A comparative study for aqueous electrolyte solutions".
      Journal of Molecular Liquids 212(103–110), 2015.
      [PDF] (792 KB) [DOI]
    • Lesch, Volker and Heuer, Andreas and Holm, Christian and Smiatek, Jens.
      "Solvent effects of 1-ethyl-3-methylimidazolium acetate: solvation and dynamic behavior of polar and apolar solutes".
      Physical Chemistry Chemical Physics 17(8480–8490), 2015.
      [PDF] (3 MB) [DOI]
    • Wohlfarth, Andreas and Smiatek, Jens and Kreuer, Klaus-Dieter and Takamuku, Shogo and Jannasch, Patric and Maier, Joachim.
      "Proton Dissociation of Sulfonated Polysulfones: Influence of Molecular Structure and Conformation".
      Macromolecules 48(4)(1134–1143), 2015.
      [PDF] (2 MB) [DOI]
    • Zhou, Jiajia and Smiatek, Jens and Asmolov, Evgeny S and Vinogradova, Olga I and Schmid, Friederike.
      "Application of Tunable-Slip Boundary Conditions in Particle-Based Simulations".
      High Performance Computing in Science and Engineering '14 , 2014.
      Springer.
    • Heuer, Andreas and Smiatek, Jens and Strauss, Bernd and Riedl, Dennis.
      "Informationsgehalt von Fussball-Spieldaten".
      In Fussball in Forschung und Lehre - Beiträge und Analysen zum Fusballsport XIX, volume of Schriften der Deutschen Vereinigung für Sportwissenschaft Band 240.
      Czwalina, 2014.
    • Narayanan Krishnamoorthy, Anand and Holm, Christian and Smiatek, Jens.
      "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] (2 MB) [DOI]
    • Micciulla, Samantha and Sánchez, Pedro A. and Smiatek, Jens and Qiao, Baofu and Sega, Marcello and Laschewsky, André and Holm, Christian and von Klitzing, Regine.
      "Layer-by-Layer Formation of Oligoelectrolyte Multilayers: A Combined Experimental and Computational Study".
      Soft Materials 12(sup1)(S14–S21), 2014.
      [PDF] (581 KB) [DOI]
    • Hickey, Owen A. and Holm, Christian and Smiatek, Jens.
      "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]
    • Smiatek, Jens and Heuer, Andreas.
      "Deprotonation mechanism of a single-stranded DNA i-motif".
      RSC Advances 4(17110–17113), 2014.
      [PDF] (380 KB) [DOI]
    • Matthias U. Bohner and Johannes Zeman and Jens Smiatek and Axel Arnold and Johannes Kästner.
      "Nudged-elastic band used to find reaction coordinates based on the free energy".
      Journal of Chemical Physics 140(7)(074109), 2014.
      [PDF] (637 KB) [DOI]
    • Jens Smiatek and Andreas Wohlfarth and 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] [URL]
    • Smiatek, Jens.
      "Osmolyte Effects: Impact on the Aqueous Solution around Charged and Neutral Spheres".
      The Journal of Physical Chemistry B 118(3)(771–782), 2014.
      [PDF] (2 MB) [DOI]
    • Smiatek, Jens and Janssen-Müller, Daniel and Friedrich, Rudolf and Heuer, Andreas.
      "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]
    • Smiatek, J. and Harishchandra, R. K. and Galla, H.-J. and Heuer, A..
      "Low Concentrated Hydroxiectoine Solutions in Presence of DPPC Lipid Bilayers: A Computer Simulation Study".
      Biophysical Chemistry 180(102–109), 2013.
      [PDF] (895 KB) [DOI]
    • Smiatek, Jens and Heuer, Andreas and Wagner, Hendrik and Studer, Armido and Hentschel, Carsten and Chi, Lifeng.
      "Coat thickness dependent adsorption of hydrophobic molecules at polymer brushes".
      Journal of Chemical Physics 138(4), 2013.
      [PDF] (759 KB) [DOI]
    • Hentschel, Carsten and Wagner, Hendrik and Smiatek, Jens and Heuer, Andreas and Fuchs, Harald and Zhang, Xi and Studer, Armido and Chi, Lifeng.
      "AFM-based Force Spectroscopy on Polystyrene Brushes: Effect of Brush Thickness on Protein Adsorption".
      Langmuir 29(1850–1856), 2013.
    • Smiatek, Jens and Liu, Dongsheng and Heuer, Andreas.
      "Unfolding pathways and the free energy landscape of a single-stranded DNA i-motif".
      In From Computational Biophysics to Systems Biology (CBSB11), volume of IAS-Series.
      NIC-Publishing, 2012.
    • Meinhardt, Sebastian and Smiatek, Jens and Eichhorn, Ralf and Schmid, Friederike.
      "Separation of Chiral Particles in Micro- or Nanofluidic Channels".
      Physical Review Letters 108(214504), 2012.
      [PDF] (493 KB) [DOI]
    • Jens Smiatek and Rakesh Kumar Harishchandra and Oliver Rubner and Hans-Joachim Galla and Andreas Heuer.
      "Properties of compatible solutes in aqueous solution".
      Biophysical Chemistry 160(1)(62–68), 2012.
      [PDF] (856 KB) [DOI]
    • Jens Smiatek and Friederike Schmid.
      "Mesoscopic Simulation Methods for Studying Flow and Transport in Electric Fields in Micro- and Nanochannels".
      In Advances in Microfluidics, chapter 5. Editors: Ryan T. Kelly,
      InTech, 2012.
      [PDF] (427 KB) [DOI] [URL]
    • Smiatek, Jens and Liu, Dongsheng and Heuer, Andreas.
      "High temperature unfolding simulations of a single-stranded DNA i-motif".
      Current Physical Chemistry 2(115–123), 2012.
    • Smiatek, Jens and Chen, Chun and Liu, Dongsheng and Heuer, Andreas.
      "Stable Conformations of a Single Stranded Deprotonated DNA i-Motif".
      Journal of Physical Chemistry B 115(46)(13788–13795), 2011.
      [PDF] (5 MB) [DOI] [URL]
    • Smiatek, Jens and Schmid, Friederike.
      "Mesoscopic Simulations of Polyelectrolyte Electrophoresis in Nanochannels".
      In High Performance Computing in Science and Engineering '10, pages 53–67. Editors: Nagel, Wolfgang E. and Kröner, Dietmar B. and Resch, Michael M.,
      Springer Berlin Heidelberg, 2011.
      [DOI]
    • Smiatek, Jens and Heuer, Andreas.
      "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 and Friederike Schmid.
      "Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels".
      Computer Physics Commications 182(9)(1941–1944), 2011.
      Computer Physics Communications Special Edition for Conference on Computational Physics Trondheim, Norway, June 23-26, 2010
      [PDF] (277 KB) [DOI] [URL]
    • Smiatek, Jens and Schmid, Friederike.
      "Polyelectrolyte Electrophoresis in Nanochannels: A Dissipative Particle Dynamics Simulation".
      Journal of Physical Chemistry B 114(19)(6266–6272), 2010.
      [PDF] (250 KB) [DOI] [URL]
    • Smiatek, Jens.
      "Mesoscopic simulations of electrohydrodynamic phenomena".
      PhD thesis, Bielefeld University, Germany, jan, 2009.
      [PDF] (2 MB)
    • Smiatek, Jens and Sega, Marcello and Holm, Christian and Schiller, Ulf D. and Schmid, Friederike.
      "Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study".
      Journal of Chemical Physics 130(244702), 2009.
      [PDF] (370 KB) [DOI]
    • Smiatek, Jens and Allen, Michael P. and Schmid, Friederike.
      "Tunable-slip boundaries for coarse-grained simulations of fluid flow".
      European Physical Journal E: Soft Matter 26(115–122), 2008.
      [PDF] (179 KB)


Submitted Manuscripts

  • Weyman, A.: Bier, M.; Holm, C.; Smiatek, J.
    Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: a coarse-grained molecular dynamics study, submitted (2017)
  • Uhlig, F.; Zeman, J.; Smiatek, J.; Holm, C.
    First-principles parameterization of polarizable coarse-grained force fields for ionic liquids, submitted (2017)
  • Oprzeska-Zingrebe, E. A.; Smiatek, J.
    Thermodynamic aspects concerning the preferential binding of urea to single-stranded DNA structures: a molecular dynamics simulation study, submitted (2017)
  • Ribeiro Tzaras, E.; Weik, F.; Holm, C.; Smiatek, J.
    Polymer translocation through thin nano pores: An unbiased perspective on free energy landscapes and essential dynamics, submitted (2016)
  • Smiatek, J.; Riedl, D.; Heuer, A.
    Statistical properties of soccer, basketball and handball - A quantitative comparison, submitted (2016)
Retrieved from "https://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Jens_Smiatek&oldid=22845"