Difference between revisions of "Jens Smiatek"

From ICPWiki
Jump to navigation Jump to search
Line 43: Line 43:
 
== Publications ==
 
== Publications ==
 
My profile at [http://scholar.google.de/citations?user=-RgaRekAAAAJ "Scholar Google"]
 
My profile at [http://scholar.google.de/citations?user=-RgaRekAAAAJ "Scholar Google"]
−
 
+
:* Landsgesell, J.; Holm, C.; Smiatek, J.
 +
:: '''The Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.'''
 +
:: Accepted for publication in ''J. Chem. Theory Comput.'' (2016)
 
:* Landsgesell, J.; Holm, C.; Smiatek, J.
 
:* Landsgesell, J.; Holm, C.; Smiatek, J.
 
:: '''Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method.'''
 
:: '''Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method.'''
Line 99: Line 101:
 
* Smiatek, J.; Riedl, D.; Heuer, A.
 
* Smiatek, J.; Riedl, D.; Heuer, A.
 
*: Statistical properties of soccer, basketball and handball - A quantitative comparison, submitted (2016)
 
*: Statistical properties of soccer, basketball and handball - A quantitative comparison, submitted (2016)
−
 
−
* Landsgesell, J.; Holm, C.; Smiatek, J.
 
−
*: The Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions, submitted (2016)
 
  
 
* Michalowsky, J.; Schäfer, L. V.; Holm, C.; Smiatek, J.
 
* Michalowsky, J.; Schäfer, L. V.; Holm, C.; Smiatek, J.
 
*: A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions, submitted (2016)
 
*: A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions, submitted (2016)

Revision as of 22:19, 28 December 2016

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"

  • Landsgesell, J.; Holm, C.; Smiatek, J.
The Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.
Accepted for publication in J. Chem. Theory Comput. (2016)
  • Landsgesell, J.; Holm, C.; Smiatek, J.
Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method.
Accepted for publication in Europ. Phys. J. Spec. Top. (2016)
  • Jens Smiatek, Niels Hansen, Johannes Kästner.
    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. ISBN: 978-1-78262-429-5.
    [DOI] [URL]
  • Martin A. Schroer, Julian Michalowsky, Birgit Fischer, Jens Smiatek, Gerhard Grübel.
    Stabilizing Effect of TMAO on Globular PNIPAM States: Preferential Attraction Induces Preferential Hydration.
    Physical Chemistry Chemical Physics 18(46):31459–31470, 2016.
    [PDF] (2.6 MB) [DOI]
  • Anand Narayanan Krishnamoorthy, Johannes Zeman, Christian Holm, Jens Smiatek.
    Preferential solvation and ion association properties in aqueous dimethyl sulfoxide solutions.
    Physical Chemistry Chemical Physics 18(45):31312–31322, 2016.
    [PDF] (3.6 MB) [DOI]
  • Volker Lesch, Andreas Heuer, Babak R. Rad, Martin Winter, Jens Smiatek.
    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(41):28403–28408, 2016.
    [PDF] (2.3 MB) [DOI] [URL]
  • Marc Benjamin Hahn, Frank Uhlig, Tihomir Solomun, Jens Smiatek, Heinz Sturm.
    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] (2.2 MB) [DOI]
  • Konrad Breitsprecher, Anand Narayanan Krishnamoorthy, Jens Smiatek, Christian Holm.
    Force Field Optimization for Ionic Liquids: FFOIL.
    In High Performance Computing in Science and Engineering '15, pages 101–117.
    Springer, 2016.
    [PDF] (1.2 MB) [DOI]
  • Pedro A. Sánchez, Jens Smiatek, Qiao Baofu, Marcello Sega, Christian Holm.
    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. Edited by E. Wolfgang Nagel, H. Dietmar Kröner, M. Michael Resch.
    Springer International Publishing, 2016. ISBN: 978-3-319-24633-8.
    [PDF] (292 KB) [DOI]
  • Samantha Micciulla, Julian Michalowsky, Martin A. Schroer, Christian Holm, Regine von Klitzing, Jens Smiatek.
    Concentration dependent effects of urea binding to poly(N-isopropylacrylamide) brushes: a combined experimental and numerical study.
    Physical Chemistry Chemical Physics 18(7):5324–5335, 2016.
    [PDF] (2.4 MB) [DOI]
  • Volker Lesch, Andreas Heuer, Christian Holm, Jens Smiatek.
    Properties of Apolar Solutes in Alkyl Imidazolium-Based Ionic Liquids: The Importance of Local Interactions.
    ChemPhysChem 17(3):387–394, 2016.
    [PDF] (1.2 MB) [DOI]
  • Martin Vögele, Christian Holm, Jens Smiatek.
    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, Tihomir Solomun, Robert Wellhausen, Sabrina Hermann, Harald Seitz, Susann Meyer, Hans-Jörg Kunte, Johannes Zeman, Frank Uhlig, Jens Smiatek, 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]
  • Florian Fahrenberger, Owen A. Hickey, Jens Smiatek, Christian Holm.
    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] (1.9 MB) [DOI]
  • Volker Lesch, Andreas Heuer, Vasileios A. Tatsis, Christian Holm, Jens Smiatek.
    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] (1.8 MB) [DOI]
  • Florian Fahrenberger, Owen A. Hickey, Jens Smiatek, Christian Holm.
    Importance of varying permittivity on the conductivity of polyelectrolyte solutions.
    Physical Review Letters 115(11):118301, 2015.
    [PDF] (523 KB) [DOI]
  • Martin Vögele, Christian Holm, Jens Smiatek.
    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]
  • 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

  • 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)
  • Michalowsky, J.; Schäfer, L. V.; Holm, C.; Smiatek, J.
    A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions, submitted (2016)
Retrieved from "https://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Jens_Smiatek&oldid=21475"