About

Basic information:

name: Eva Pluhařová

current position:
Postdoctoral researcher at J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech RepublicEva-Jan2017

address:
Dolejškova 2155/3
182 23 Praha 8
Czech Republic

phone: +420 26605 2077
email: eva.pluharova(at)jh-inst.cas.cz
born: 6. 2. 1986 in Ostrov, Czech Republic

Research interests:

Computer simulations of (bio)molecules in aqueous solution, understanding how their properties and electronic structure change upon hydration, importance of water for functioning of biomolecules.

  • Enzyme catalysis in non-aqueous solvent
  • Influence of solute on water dynamics
  • Photoionisation of nucleic acid bases and how is this process influenced by presence of sugar, phosphate, counterions and water
  • Modeling of ion solvation
  • Ion-ion and ion-peptide bond interactions

Computational methods:

  • Ab initio calculations
  • Born-Oppenheimer molecular dynamics simulations
  • Classical molecular dynamics simulation with empirical force fields
  • Enhanced sampling techniques

Highlights and grants:

  • Chair of the Water & Aqueous Solutions Gordon Research Seminar 2018
  • Zdeněk Herman prize for a Ph.D. thesis 2015
  • Skinner poster prize at Faraday Discussion 160 2012
  • Junior grant of the Czech Science Foundation (Solvent effects in non-aqueous biocatalysis) 01/2017 – 12/2019
  • Postdoctoral support of the Czech Academy of Sciences (Modelování vlivu reakčního prostředí na biokatalýzu) 10/2016 – 9/2018

Education:

  • 2010-2014 Ph.D. student at Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic in Prague in the group of Prof. Pavel Jungwirth
    also at Charles University in Prague, Faculty of Science, Department of Physical and Macromolecular Chemistryand in International Max Planck Research School “Dynamical Processes in Atoms, Molecules and Solids” in Dresden
  • 2008-2010 Master of Science, Studies in Chemistry at the Faculty of Science of the Charles University in Prague.
    Diploma thesis: Molecular simulations of ice nucleation (advisor Prof. Pavel Jungwirth)
  • 2008-2010 Master of Science, Studies in Chemistry and Chemical Engineering at the Faculty of Chemical Engineering of Institute of Chemical Technology in Prague.
    Diploma thesis: Radiation damage in biomolecules: Ionization of nucleic acid components (advisor Prof. Petr Slavíček)
  • 2005-2008 Bachelor of Science, Studies in Chemistry at the Faculty of Science of the Charles University in Prague.
    Bachelor thesis: The onset of ion solvation by ab initio calculations: Comparison between water and methanol (advisor Prof. Pavel Jungwirth)
  • 2005-2008 Bachelor of Science, Studies in Chemistry and Chemical Engineering at the Faculty of Chemical Engineering of Institute of Chemical Technology in Prague.
    Bachelor thesis: Atmospheric water nanoclusters (advisor Prof. Petr Slavíček)

Experience:

  • 10/2014 – 9/2016 postdoctoral researcher at École Normale Supérieure Paris, France
    in the group of Prof. Damien Laage
  • 2016 (1 week) Freie Universität Berlin, Germany, in the group of  PD Dr. Burkhard Schmidt
  • 2014 (1 week) Freie Universität Berlin, Germany, in the group of PD Dr. Burkhard Schmidt
  • 2013 (2 months) Pacific Northwest National Laboratory, Richland, USA with Dr.  Christopher J. Mundy
    1 week  École Normale Supérieure Paris, France, in the group of Prof. Damien Laage
    2 weeks Freie Universität Berlin, Germany, in the group of  PD Dr. Burkhard Schmidt
  • 2012 (4 weeks) Freie Universität Berlin, Germany, in group of PD Dr. Burkhard Schmidt
    1 week at USC, Los Angeles, USA, in the group of Prof. Stephen E. Bradforth
    1 week at UC, Irvine, USA, in the group of Prof. Barbara Finlayson-Pitts
  • 2011 (3 weeks) Freie Universität Berlin, Germany, in the group of PD Dr. Burkhard Schmidt
  • 2011 (3 months) advanced level course “Statistical Mechanics with focus on Liquids, Solutions and Colloidal Systems” at the University of Gothenburg, Sweden.

Teaching:

  • Exercises for the lecture Metody molekulové dynamiky a Monte Carlo (Methods of Molecular Dynamics and Monte Carlo) 2010, 2011, 2012, 2013.
  • One lesson of  the lecture Pokročilé metody molekulové dynamiky a Monte Carlo (Advanced Methods of Molecular Dynamics and Monte Carlo) 2012 [handout.pdf], 2013 [handout2013].
  • Consultant of two bachelor theses defended in June 2014:
    Photoionization of the 8-oxoguanine and derived nucleosides and nucleotides in the aqueous environment (Vladimír Palivec)
    Interaction of alkali metal and halide ions with the peptide bond
    (Tomáš Martinek)

Other:

Mendeley profile:

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