Research Interest

At present, my research is focused on computer simulation of soft and biological matter. The focus is both on developing new simulation techniques and their application to complex molecular systems.

Multiscale Modeling & Simulation

Soft and biological matter is characterized by physical properties that are determined by the interplay of disparate length and time scales. Multiscale simulation techniques that couple multiple models at different resolutions provide the most efficient way to span many orders of magnitude in the spatiotemporal scales involved in these systems.

  • AdResS: Adaptive Resolution Simulation
  • SWINGER: Dynamic Clustering Algorithm
  • STOCK: Structure Mapper and Online Coarse-Graining Kit for Molecular Simulations
  • Coupling Atomistic and Continuum Hydrodynamics

Open Boundary Molecular Dynamics

Open molecular systems exchange mass, momentum, and energy with their surroundings. Our OBMD methodology enables us to perform equilibrium molecular dynamics simulations in the grand-canonical ensemble as well as nonequilibrium fluid flow simulations. The flow is introduced via an external boundary condition while the equations of motion for the bulk remain unaltered.

Nanofluidics

We simulate fluid flows past and through nano-objects using computational fluid dynamics aiming to reproduce essential features of the fluid flows computed by molecular dynamics. Computational advantages of computational fluid dynamics allow for simulations well beyond the current reach of molecular dynamics.


  • All
  • AdResS
  • SWINGER
  • STOCK
  • OBMD
  • AT-CO
  • NANO

Adaptive resolution simulation of an atomistic protein in MARTINI water

We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly.

Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Article:
J. Chem. Phys. 140, 054114, 2014
Authors:
  • Julija Zavadlav
  • Manuel N. Melo
  • Siewert J. Marrink
  • Matej Praprotnik

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Adaptive resolution simulation of a DNA molecule in salt solution

We present a multiscale simulation of a DNA molecule in 1 M NaCl salt solution environment, employing the adaptive resolution simulation approach that allows the solvent molecules, i.e., water and ions, to change their resolution from atomistic to coarse-grained and vice versa adaptively on-the-fly.

Article:
J. Chem. Theory Comput. 11, 5035-5044, 2015
Authors:
  • Julija Zavadlav
  • Rudolf Podgornik
  • Matej Praprotnik

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Adaptive resolution simulation of a DNA molecule in MARTINI salt solution

We present a dual-resolution model of a DNA molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent.

Article:
Eur. Phys. J. Special Topics, DOI: 10.1140/epjst/e2016-60117-8
Authors:
  • Julija Zavadlav
  • Rudolf Podgornik
  • Manuel N. Melo
  • Siewert J. Marrink
  • Matej Praprotnik

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STOCK: Structure mapper and online coarse-graining kit for molecular simulations

available at http://stock.cmm.ki.si

Article:
J. Comput. Chem. 36, 467-477, 2015
Authors:
  • Stas Bevc
  • Christoph Junghans
  • Matej Praprotnik

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SWINGER: a dynamic clustering algorithm

SWINGER is a dynamic clustering algorithm that can concurrently assemble, disassemble, and reassemble water bundles, consisting of several water molecules. Thus, it allows for a seamless coupling between standard atomistic and supramolecular water models in adaptive resolution simulations.

SWINGER paves the way for efficient multiscale simulations of biomolecular systems without compromising the accuracy of atomistic water models.

Article:
J. Chem. Theory Comput. 12, 4138-4145, 2016
Authors:
  • Julija Zavadlav
  • Siewert J. Marrink
  • Matej Praprotnik

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Open boundary molecular dynamics

The core domain of the simulation box is solved using the all-atom resolution. The coarse-grained layer introduced by AdResS is located at the outer part of the open simulation box to enable the insertion of large molecules into the system.

Article:
Eur. Phys. J. Special Topics 224, 2331-2349, 2015
Authors:
  • Rafael Delgado-Buscalioni
  • Jurij Sablic
  • Matej Praprotnik

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Continuum simulations of water flow in carbon nanotube membranes

We propose the use of the Navier–Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes.

Article:
New J. Phys. 16, 082001, 2014
Authors:
  • Aleksandar Popadic
  • Jens H. Walther
  • Petros Koumoutsakos
  • Matej Praprotnik

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