Address

Chair of Computational Science
Clausiusstrasse 33
ETH-Zentrum, CLT E 13
CH-8092 Zürich

Contact Information

Email: julijaz@ethz.ch

Julija Zavadlav

Post-doctoral Fellow

Research and Interests

  • Molecular modeling
  • Uncertainty Quantification
  • Multiscale simulations

Education

  • Ph.D. Physics, University of Ljubljana, Slovenia, 2015
  • B.S. Physics, University of Ljubljana, Slovenia, 2011

Publications

2018

  • J. Zavadlav, J. Sablić, R. Podgornik, and M. Praprotnik, “Open-boundary molecular dynamics of a dna molecule in a hybrid explicit/implicit salt solution,” Biophys. j., vol. 114, iss. 10, p. 2352–2362, 2018.
    [BibTeX] [DOI]
    @article{Zavadlav:2018b,
    author = {Zavadlav, Julija and Sablić, Jurij and Podgornik, Rudolf and Praprotnik, Matej},
    title = {Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution},
    journal = {Biophys. J.},
    volume = {114},
    number = {10},
    pages = {2352–2362},
    year = {2018},
    doi = {doi.org/10.1016/j.bpj.2018.02.042},
    URL = {https://doi.org/10.1016/j.bpj.2018.02.042}
    }

  • J. Zavadlav, S. J. Marrink, and M. Praprotnik, “Multiscale simulation of protein hydration using the swinger dynamical clustering algorithm,” Journal of chemical theory and computation, vol. 14, iss. 3, pp. 1754-1761, 2018.
    [BibTeX] [DOI]
    @article{Zavadlav:2018a,
    author = {Zavadlav, Julija and Marrink, Siewert J. and Praprotnik, Matej},
    title = {Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm},
    journal = {Journal of Chemical Theory and Computation},
    volume = {14},
    number = {3},
    pages = {1754-1761},
    year = {2018},
    doi = {10.1021/acs.jctc.7b01129},
    URL = {http://dx.doi.org/10.1021/acs.jctc.7b01129}
    }

  • R. Podgornik, J. Zavadlav, and M. Praprotnik, “Molecular dynamics simulation of high density dna arrays,” Computation, vol. 6, iss. 1, p. 3, 2018.
    [BibTeX] [DOI]
    @article{Podgornik:2018,
    author = {Podgornik, Rudolf and Zavadlav, Julija and Praprotnik, Matej},
    title = {Molecular Dynamics Simulation of High Density DNA Arrays},
    journal = {Computation},
    volume = {6},
    number = {1},
    pages = {3},
    year = {2018},
    doi = {10.3390/computation6010003},
    URL = {https://doi.org/10.3390/computation6010003}
    }

2017

  • J. Zavadlav and M. Praprotnik, “Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics,” The journal of chemical physics, vol. 147, iss. 11, p. 114110, 2017.
    [BibTeX] [DOI]
    @article{Zavadlav:2017c,
    author = {Julija Zavadlav and Matej Praprotnik},
    title = {Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics},
    journal = {The Journal of Chemical Physics},
    volume = {147},
    number = {11},
    pages = {114110},
    year = {2017},
    doi = {10.1063/1.4986916},
    URL = {https://doi.org/10.1063/1.4986916}
    }

  • J. Zavadlav, S. Bevc, and M. Praprotnik, “Adaptive resolution simulations of biomolecular systems,” European biophysics journal, vol. 46, iss. 8, pp. 821-835, 2017.
    [BibTeX] [DOI]
    @article{Zavadlav:2017b,
    author = {Julija Zavadlav and Bevc, Sta{\v{s}} and Matej Praprotnik},
    title = {Adaptive resolution simulations of biomolecular systems},
    journal = {European Biophysics Journal},
    volume = {46},
    number = {8},
    pages = {821-835},
    year = {2017},
    doi = {10.1007/s00249-017-1248-0},
    URL = {https://doi.org/10.1007/s00249-017-1248-0}
    }

  • J. Zavadlav, R. Podgornik, and M. Praprotnik, “Order and interactions in dna arrays: multiscale molecular dynamics simulation,” Scientific reports, vol. 7, iss. 1, pp. 4775-4786, 2017.
    [BibTeX] [DOI]
    @article{Zavadlav:2017a,
    author = {Julija Zavadlav and Podgornik, Rudolf and Matej Praprotnik},
    title = {Order and interactions in DNA arrays: Multiscale molecular dynamics simulation},
    journal = {Scientific Reports},
    volume = {7},
    number = {1},
    pages = {4775-4786},
    year = {2017},
    doi = {10.1038/s41598-017-05109-2},
    URL = {https://doi.org/10.1038/s41598-017-05109-2}
    }

2016

  • J. Zavadlav, S. J. Marrink, and M. Praprotnik, “Adaptive resolution simulation of supramolecular water: the concurrent making, breaking, and remaking of water bundles,” Journal of chemical theory and computation, vol. 12, iss. 8, pp. 4138-4145, 2016.
    [BibTeX] [DOI]
    @article{Zavadlav:2016b,
    author = {Zavadlav, Julija and Marrink, Siewert J. and Praprotnik, Matej},
    title = {Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles},
    journal = {Journal of Chemical Theory and Computation},
    volume = {12},
    number = {8},
    pages = {4138-4145},
    year = {2016},
    doi = {10.1021/acs.jctc.6b00536},
    URL = {http://dx.doi.org/10.1021/acs.jctc.6b00536}
    }

  • J. Zavadlav, R. and Podgornik, M. N. Melo, S. J. Marrink, and M. Praprotnik, “Adaptive resolution simulation of an atomistic dna molecule in martini salt solution,” The european physical journal special topics, vol. 225, iss. 8, pp. 1595-1607, 2016.
    [BibTeX] [DOI]
    @article{Zavadlav:2016a,
    author = {Zavadlav, Julija and and Podgornik, Rudolf and Melo, Manuel Nuno and Marrink, Siewert J. and Praprotnik, Matej},
    title = {Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution},
    journal = {The European Physical Journal Special Topics},
    volume = {225},
    number = {8},
    pages = {1595-1607},
    year = {2016},
    doi = {10.1140/epjst/e2016-60117-8},
    URL = {https://doi.org/10.1140/epjst/e2016-60117-8}
    }

2015

  • J. Zavadlav, R. Podgornik, and M. Praprotnik, “Adaptive resolution simulation of a dna molecule in salt solution,” Journal of chemical theory and computation, vol. 11, iss. 10, pp. 5035-5044, 2015.
    [BibTeX] [DOI]
    @article{Zavadlav:2015b,
    author = {Zavadlav, Julija and Podgornik, Rudolf and Praprotnik, Matej},
    title = {Adaptive Resolution Simulation of a DNA Molecule in Salt Solution},
    journal = {Journal of Chemical Theory and Computation},
    volume = {11},
    number = {10},
    pages = {5035-5044},
    year = {2015},
    doi = {10.1021/acs.jctc.5b00596},
    URL = {http://dx.doi.org/10.1021/acs.jctc.5b00596}
    }

  • J. Zavadlav, M. N. Melo, S. J. Marrink, and M. Praprotnik, “Adaptive resolution simulation of polarizable supramolecular coarse-grained water models,” The journal of chemical physics, vol. 142, iss. 24, p. 244118, 2015.
    [BibTeX] [DOI]
    @article{Zavadlav:2015a,
    author = {Julija Zavadlav and Manuel N. Melo and Siewert J. Marrink and Matej Praprotnik},
    title = {Adaptive resolution simulation of polarizable supramolecular coarse-grained water models},
    journal = {The Journal of Chemical Physics},
    volume = {142},
    number = {24},
    pages = {244118},
    year = {2015},
    doi = {10.1063/1.4923008},
    URL = {https://doi.org/10.1063/1.4923008}
    }

2014

  • J. Zavadlav, M. N. Melo, A. V. Cunha, A. H. de Vries, S. J. Marrink, and M. Praprotnik, “Adaptive resolution simulation of martini solvents,” Journal of chemical theory and computation, vol. 10, iss. 6, pp. 2591-2598, 2014.
    [BibTeX] [DOI]
    @article{Zavadlav:2014b,
    author = {Zavadlav, Julija and Melo, Manuel N. and Cunha, Ana V. and de Vries, Alex H. and Marrink, Siewert J. and Praprotnik, Matej},
    title = {Adaptive Resolution Simulation of MARTINI Solvents},
    journal = {Journal of Chemical Theory and Computation},
    volume = {10},
    number = {6},
    pages = {2591-2598},
    year = {2014},
    doi = {10.1021/ct5001523},
    URL = {http://dx.doi.org/10.1021/ct5001523}
    }

  • J. Zavadlav, M. N. Melo, S. J. Marrink, and M. Praprotnik, “Adaptive resolution simulation of an atomistic protein in martini water,” The journal of chemical physics, vol. 140, iss. 5, p. 54114, 2014.
    [BibTeX] [DOI]
    @article{Zavadlav:2014a,
    author = {Julija Zavadlav and Manuel Nuno Melo and Siewert J. Marrink and Matej Praprotnik},
    title = {Adaptive resolution simulation of an atomistic protein in MARTINI water},
    journal = {The Journal of Chemical Physics},
    volume = {140},
    number = {5},
    pages = {054114},
    year = {2014},
    doi = {10.1063/1.4863329},
    URL = {https://doi.org/10.1063/1.4863329}
    }