Education

2003

Ph.D. Physics, University of Ljubljana, Slovenia

1998

B.S. Physics, University of Ljubljana, Slovenia

Professional Experience

2017 - Present

Acting Head of Department

Department of Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia

2016 - Present

Senior Research Adviser

Department of Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia

2013 - Present

Associate Professor of Physics

Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Slovenia

2008 - 2013

Assistant Professor of Physics

Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Slovenia

2004 - 2008

Postdoctoral Researcher

Theory Group, Max Planck Institute for Polymer Research, Mainz, Germany

2003 - 2016

(Senior, Postdoctoral) Research Associate

Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia

2002 - 2005

Teaching Assistant of Physics

Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Slovenia

1998 - 2003

Young Researcher

Laboratory for Molecular Modelling and NMR Spectroscopy, National Institute of Chemistry, Ljubljana, Slovenia

Visiting Positions

2013

Visiting Scientist (1 month)

Kavli Institute for Theoretical Physics China at the Chinese Academy of Sciences, Beijing, China

2012

Member (2 months)

The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, USA

2009 - 2010

Academic Guest (6 months)

Chair of Computational Science, ETH Zurich, Zurich, Switzerland

2008

General Member (1 month)

Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, USA

Teaching Experience

Supervision

5 Ph.D. and 2 undergraduate students

Fellowships and Grants

2017 - Present

"Mathematical and Simulation Methods in Studies of Molecular Structure and Dynamics and Non-Equilibrium Statistical Mechanics"

Program Leader, 5-year Basic Research Program P1-0002 funded by Slovenian Research Agency

2011 - 2015

"Computer Simulations of Fluid Flow - Matter Interactions at Multiple Length Scales"

Project Leader, 3-year Basic Research Project J1-4134 funded by Slovenian Research Agency

2011 - 2012

"Multiscale Simulations of Fluid Flows"

Principal Investigator, 2-year Bilateral Project BI-DK/11-12-002 between Slovenia and Denmark funded by Slovenian Research Agency

2009 - 2012

"Development and Application of Multiscale Modeling Approaches for Simulation of Soft Matter"

Project Leader, 3-year Basic Research Project J1-2281 funded by Slovenian Research Agency

Honors and Awards

2004

The National Institute of Chemistry Award for Exceptional Doctoral Work

Professional Activities

2016 - Present

Member

PRACE Scientific Steering Committee (SSC)

2015 - Present

President

Slovenian Biophysical Society

2011 - 2015

Member

Executive Board of the Slovenian Biophysical Society

Personal Details

Name
Prof. Dr. Matej Praprotnik
Address
Department of Molecular Modeling
National Institute of Chemistry
Hajdrihova 19
SI-1001 Ljubljana
Slovenia
E-mail
praprot@cmm.ki.si
Download my CV

Invited Talks and Lectures

  • Adaptive resolution simulations coupling atomistic to supramolecular water. PASC17, Palazzo dei Congressi, Lugano, Switzerland, June 26-28, 2017.
  • Multiscale simulations of DNA. Bioorigami – designed bionanostructures from nucleic acids to proteins and beyond, National Institute of Chemistry, Ljubljana, Slovenia, June 21-23, 2017.
  • Open Boundary Molecular Dynamics Simulation. Seminar SBP, SISSA, Trieste, Italy, June 8, 2017.
  • Adaptive resolution simulations of supramolecular water. E-CAM Workshop: State of the art in mesoscale and multiscale modeling, CECAM-IRL, University College Dublin, Dublin, Ireland, May 29 - June 1, 2017.
  • Adaptive resolution simulations of DNA. Multiscale Modeling and Experimental Approaches to Genome Organization, Ecole de Physique, Les Houches, France, April 2-7, 2017.
  • Adaptive resolution simulations of supramolecular water models. First Workshop on Hybrid Methods in Molecular Simulation, University of Cagliari, Cagliari, Italy, April 3-4, 2017.
  • Open Boundary Molecular Dynamics. Scaling Cascades in Complex Systems, FU Berlin, Berlin, Germany, March 27-29, 2017.
  • Concurrent coupling of atomistic and supramolecular water models. COST Action MP1305 Flowing Matter WG2+WG3 Meeting, Erlangen, Germany, February 28-March 3, 2017.
  • Adaptive resolution simulations coupling atomistic models to MARTINI. Multiscale Simulation Methods in Soft Matter Systems II, Darmstadt, Germany, October 4-6, 2016.
  • Open boundary molecular dynamics of star-polymer melts. The 12th World Congress on Computational Mechanics and The 6th Asia-Pacific Congress on Computational Mechanics, Seoul, Korea, July 24-29, 2016.
  • Adaptive resolution simulation of supramolecular water models. 2016 SIAM Conference on Mathematical Aspects of Material Science, Philadelphia, Pennsylvania, USA, May 8-12, 2016.
  • Adaptive resolution simulation of polarizable supramolecular water models. 13th US National Congress on Computational Mechanics, San Diego, CA, USA, July 26-30, 2015.
  • Adaptive resolution simulations of supramolecular coarse-grained water models. ZCAM Workshop: Molecular Hydrodynamics Meets Fluctuating Hydrodynamics, Residencia La Cristalera, Miraflores de la Sierra, Madrid, Spain, May 10-14, 2015.
  • Napredne metode simulacij molekulske dinamike - vecskalne simulacije z uporabo polja sil MARTINI, odprte simulacije molekulske dinamike in hibridne metode za simulacijo nanofluidike. 2. mednarodna spomladanska sola fizike - delavnice iz biofizike, Maribor, Slovenia, May 5-12, 2015.
  • Simulacije z uporabo metode AdResS: sklopitev atomisticne in grobozrnate resolucije. 2. mednarodna spomladanska sola fizike - delavnice iz biofizike, Maribor, Slovenia, May 5-12, 2015.
  • Multiscale simulations of water flow past/through nanoscale objects. CECAM Workshop: Scale-Bridging Techniques in Molecular Simulation: A Critical Appraisal, Zuse-Institut Berlin (ZIB), Berlin, Germany, August 25-27, 2014.
  • Adaptive resolution simulation of atomistic protein in multiscale water. 11th World Congress on Computational Mechanics (WCCM XI) and 5th European Conference on Computational Mechanics (ECCM V) and 6th European Conference on Computational Fluid Dynamics (ECFD VI), Barcelona, Spain, July 20-25, 2014.
  • Open molecular dynamics simulation of star polymers. III International Conference on Particle-Based Methods. Fundamentals and Applications (Particles 2013), Stuttgart, Germany, September 18-20, 2013.
  • Open molecular dynamics simulation of star polymers. Austrian-Slovenian Polymer Meeting (ASPM 2013), Bled, Slovenia, April 3-5, 2013.
  • Adaptive resolution simulations coupled to continuum. IUTAM Symposium on Particle Methods in Fluid Mechanics, Technical University of Denmark, Kgs. Lyngby, Denmark, October 15-16, 2012.
  • Multiscale simulation of liquids. 12th International Conference Computational and Mathematical Methods in Science and Engineering (CMMSE), La Manga - Murcia, Spain, July 2-5, 2012.
  • Coupling atomistic and continuum hydrodynamics. Modeling Soft Matter: Linking Multiple Length and Time Scales, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, USA, June 4-8, 2012.
  • Concurrent multiscale simulation of molecular liquids. CECAM Workshop: Multiscale Modeling of Simple and Complex Liquid Flow Using Particle-Continuum Hybrids, ZCAM, Zaragoza, Spain, October 5-7, 2011.
  • Multiscale simulation methods for liquids. Cambridge-Edinburgh Meeting, Department of Chemistry, University of Cambridge, Cambridge, UK, April 26-27, 2011.
  • Multiscale simulations of fluids. INRIA, Grenoble, France, April 20, 2011.
  • Hybrid methods for multiscale simulation of liquids. ETHZ - CECAM - ESF Workshop in Multiscale Modeling and Simulation, Kartause Ittingen, Switzerland, October 19-22, 2010.
  • Linking atomistic and continuum hydrodynamics. Novel Simulation Approaches to Soft Matter Systems Workshop, Dresden, Germany, September 20-24, 2010.
  • Hybrid methods for multiscale flow simulations. Regional Biophysics Conference 2010, Primosten, Croatia, September 15-18, 2010.
  • AdResS: Concurrent coupling of different levels of resolution in molecular simulations. 2010 Workshop on Multiscale Molecular Modelling: Molecular Dynamics, Computational Statistical Mechanics, and Simulation Algorithms, University of Edinburgh, Edinburgh, UK, June 30 - July 3, 2010.
  • Linking length scales in molecular simulations. ACAM Workshop: Dynamic Coarse-Graining: Towards Quantitative Mesoscale Modeling of Complex Fluids, ACAM, Dublin, Ireland, May 19-21, 2010.
  • Hybrid atomistic-continuum methods for dense liquids. International Autumn School "Molecular simulations at different scale - future and perspectives on modeling interfaces", Technische Universität Darmstadt, Darmstadt, Germany, September 24-25, 2009.
  • Coupling MD with continuum through a mesoscopic model. International Autumn School "Molecular simulations at different scale - future and perspectives on modeling interfaces", Technische Universität Darmstadt, Darmstadt, Germany, September 24-25, 2009.
  • Adaptive resolution simulation. The 3rd Adriatic Meeting on Computational Solutions in the Life Sciences, Primosten, Croatia, September 1-5, 2009.
  • Adaptive resolution molecular dynamics simulation. EPSRC Symposium Workshop on Molecular Dynamics, Mathematics Research Centre, University of Warwick, Coventry, UK, June 1-5, 2009.
  • Coupling atomistic and continuum hydrodynamics through a mesoscopic model. IWoM3 2009 - International Workshop on Multiscale Materials Modeling, Harnack House, Berlin, Germany, March 10-13, 2009.
  • Adaptive resolution simulation of molecular liquids. Sonderforschungsbereich (SFB) 716: Summer School "Hybridsimulationen" und Statusseminar, Universität Stuttgart, Pforzheim-Hohenwart, Germany, September 8-10, 2008.
  • Concurrent triple-scale simulation of molecular liquids. Computational Science & Engineering Laboratory, ETH Zurich, Zurich, Switzerland, May 14, 2008.
  • Adaptive resolution simulation of liquid water. New Developments in Computational Physics: CompPhys07 - 8th International NTZ Workshop, Institut für Theoretische Physik, Universität Leipzig, Leipzig, Germany, November 29 - December 1, 2007.
  • Adaptive resolution molecular dynamics simulations. Departamento de Fisica Teoretica de la Materia Condensada, Universidad Autonoma de Madrid, Madrid, Spain, May 26, 2007.
  • Fast vibrational modes in molecular simulation studies. Through Science to Stability: 1st South Eastern European Workshop on Practical Approaches to Computational Biology, Opatija, Croatia, September 1-4, 2005.
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