Matej Praprotnik

Matej Praprotnik
National Institute of Chemistry · Laboratory for Molecular Modeling

Ph.D.

About

81
Publications
11,427
Reads
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3,210
Citations
Citations since 2017
25 Research Items
1428 Citations
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2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
Introduction
At present, my research is focused on computer simulation of soft and biological matter. The focus is on developing and combining innovative computational and theoretical methods as well as their application to study complex molecular systems. My main research interests, which are at the interface of computational physics, chemistry, and applied mathematics, include: multiscale modeling and simulation, open boundary molecular simulations, and nanofluidics.
Additional affiliations
March 2020 - March 2021
Partnership for Advanced Computing in Europe
Partnership for Advanced Computing in Europe
Position
  • Chair
June 2019 - May 2021
National Institute of Chemistry
Position
  • Principal Investigator
June 2018 - present
University of Ljubljana
Position
  • Professor
Education
November 1998 - May 2003
University of Ljubljana
Field of study
  • Physics
October 1993 - May 1998
University of Ljubljana
Field of study
  • Physics

Publications

Publications (81)
Article
Full-text available
PRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations...
Article
Full-text available
We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method’s advantages and limitations in its prac...
Preprint
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution of bio-molecules remains a daunting task. In this work we present a novel framework to advance simulation time...
Article
Full-text available
Concurrent multiscale techniques such as Adaptive Resolution Scheme (AdResS) can offer ample of computational advantages over conventional atomistic (AT) Molecular Dynamics simulations. However, they typically rely on a-physical hybrid regions to maintain numerical stability when high-resolution degrees of freedom (DOFs) are randomly re-inserted at...
Article
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This work is motivated by the goal of designing simulation software for technical devices that, at their functional core, rely on atomistic‐scale processes embedded in a larger‐scale fluid environment. The core of the problem is the conceptual and technical approach for coupling particle and continuum representations of a fluid. The state of the ar...
Article
Elaborating on the tensorial conservation law for linear polymers and performing intensive Monte Carlo simulations, Aleksandar Popadić, Daniel Svenšek, Rudolf Podgornik, and Matej Praprotnik show in article number 1900019 that a generic macrosopic coupling between density and orientational order occurs already in isotropic static polymer liquids, y...
Article
In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive...
Article
Linear polymers and other connected “line liquids” exhibit a geometrical coupling between density and equilibrium orientational order on the macroscopic level that gives rise to a Meyer‐de Gennes vectorial conservation law for polar orientational order, or its amended version for apolar nematic order when described as “recovered” polar order. They...
Preprint
Full-text available
Polymers and other connected `line liquids' exhibit a coupling between density and equilibrium nematic order on the macroscopic level that gives rise to a Meyer-de Gennes {\em vectorial conservation law}. Nevertheless, in the isotropic phase they exhibit fluctuations of the density and of the nematic order that are not coupled by this vectorial con...
Article
We investigate the role of the thermodynamic (TD) force as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution molecular dynamics setup assures thermodynamic equilibrium between atomistically resolved and coarse-grained re...
Preprint
Full-text available
We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-gr...
Article
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The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: e...
Article
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We establish a macroscopic description of the splay--density coupling in semiflexible main-chain nematic polymers with hairpins, using a vectorial continuity constraint for the "recovered" polar order of the chain tangents and introducing chain backfolds (hairpins) as its new type of sources besides chain ends. We treat both types of sources on a u...
Article
To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to a modified AT water models, such as the bundled-SPC models, that use semi-harmonic springs to restrict the rel...
Article
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Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between...
Article
Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and...
Article
In this review article, we discuss and analyze some recently developed hybrid atomistic–mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained...
Article
Full-text available
The Eckart co-rotating frame is used to analyze the dynamics of star polymers under shear flow, either in melt or solution and with different types of bonds. This formalism is compared with the standard approach used in many previous studies on polymer dynamics, where an apparent angular velocity $\omega$ is obtained from relation between the tenso...
Article
Full-text available
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent order...
Article
Full-text available
Typical experimental setups for molecular systems must deal with a certain coupling to the external environment, that is, the system is open and exchanges mass, momentum, and energy with its surroundings. Instead, standard molecular simulations are mostly performed using periodic boundary conditions with a constant number of molecules. In this revi...
Article
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This work analyses the rotation of star polymers under shear flow, in melts, and in good solvent dilute solution. The latter is modeled by single molecule Brownian hydrodynamics, while melts are modeled using non-equilibrium molecular dynamics in closed (periodic) boxes and in open boundaries. A Dissipative-Particle-Dynamics (DPD) thermostat introd...
Article
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We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the o...
Article
The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to supramolecular CG models, where several molecules...
Article
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Article
Full-text available
Open Boundary Molecular Dynamics (OBMD) simulations of a sheared star polymer melt in isothermal conditions are performed to study the melt's rheology and molecular structure under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes with a fixed shear rate (using the SLODD dynamics). The OBMD...
Article
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We agree with prof. Klein [1] that there are some similarities between our method [2] and the one presented in Ref. [3] (see also Ref. [4]). There are, however, several relevant differences we would like to outline.
Article
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We present a multiscale simulation of a DNA molecule in 1M 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. The region of high resolution moves together with t...
Article
Full-text available
Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of inte...
Article
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We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as computed by the present model are in good agreement w...
Article
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This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as inte...
Article
We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, for example, all-atom, to low, that is, coarse-grained, resolution. Using...
Article
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We propose the use of the Navier–Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretizations of the Navier–Stokes equations are combined with slip lengths extracted from molecular dynamics (MD) simulations to predict the pressure losses at the CNT entranc...
Article
We present adaptive resolution molecular dynamics simulations of aqueous and apolar solvents using coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes of solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent molecules change their resolutio...
Article
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We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-gra...
Article
Full-text available
We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the othe...
Article
We review the basic theoretical principles of the adaptive resolution simulation scheme (AdResS). This method allows to change molecular resolution on-the-fly during a simulation by changing the number of degrees of freedom in specific regions of space where the required resolution is higher than in the rest of the system. We also report about rece...
Article
Recent algorithmic development of parallel force decomposition and Hamiltonian splitting methods for macromolecular simulation is described and presented.
Article
Full-text available
Simulating complex fluids or in general complex molecular systems requires approaches covering decades of time and length scales. This usually cannot be achieved within one simulation model. Over the years many different methods and models have been developed ranging from rather generic models, representing most efficiently the universal statistica...
Article
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A Comment on the Letter by S. O. Nielsen, P. B. Moore, and B. Ensing, Phys. Rev. Lett. 105, 237802 (2010). The authors of the Letter offer a Reply.
Article
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We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coe...
Article
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INTRODUCTION: We present a three-dimensional multiscale flow simulation of water past a buckyball. We employ the Schwarz alternating method to couple molecular dynamics of liquid water and the C 540 fullerene with the Lattice-Boltzmann (LB) description of the Navier-Stokes (NS) equations. Our approach allows for studying nanoscale flow phenomena th...
Article
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Simulation schemes for liquids or strongly fluctuating systems that allow to change the molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surroundings introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensur...
Article
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We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is r...
Chapter
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In this contribution we will present the survey of our past and current endeavor on parallel approaches in molecular modeling algorithm development, for example, molecular dynamics (MD) simulation. In particular, we will describe the new split integration symplectic method for the numerical solution of molecular dynamics equations and methods for t...
Chapter
Full-text available
The Adaptive Resolution Scheme (AdResS) is a simulation method, which allows to perform Molecular Dynamics (MD) simulations treating different regions with different molecular resolutions. The different scales are coupled within a unified approach by changing the number of degrees of freedom on the fly and preserving the free exchange of particles...
Article
Full-text available
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is r...
Article
The relation between atomistic structure, architecture, molecular weight and material properties is a basic concern of modern soft material science. This by now goes far beyond standard properties of bulk materials. A typical additional focus is on surface or interface aspects or on the relation between structure and function in nanoscopic molecula...
Article
Full-text available
We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions of the liquid are concurrently coupled. The presented multiscale approach, which covers the length scales ranging from the micro- to macroscale, is a combination of two dual-scale models: a particle-based adaptive resolutio...
Article
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We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-gra...
Article
Full-text available
The relation between atomistic chemical structure, molecular architecture, molecular weight, and material properties is of basic concern in modern soft material science and includes standard properties of bulk materials and surface and interface aspects, as well as the relation between structure and function in nanoscopic objects and molecular asse...
Article
A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit conside...
Article
In this contribution the survey of our past and current endeavor on molecular modeling algorithm development will be presented. In particular, symplectic integration algorithms for the numerical solution of molecular dynamics equations and methods for the determination of vibrational frequencies and normal modes of large systems will be presented....
Article
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We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, yet keeping the adv...
Article
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Water plays a central role in biological systems and processes, and is equally relevant in a large range of industrial and technological applications. Being the most important natural solvent, its presence uniquely influences biological function as well as technical processes. Because of their importance, aqueous solutions are among the most experi...
Article
Full-text available
The authors report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The...
Article
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We show how the idea of fractal dimensions of phase space variables can be employed to develop a concept of adaptive resolution treatment of a molecular liquid. The resulting theoretical framework allows for calculation of statistical averages of thermodynamic quantities in multiresolution computer simulation algorithms where the molecular degrees...
Article
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being developed. However in almost all cases, the regions treated at different level of resolution are kept fixed and do no...
Article
Full-text available
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or by far too small time scales. To overcome this problem multiscale techniques are being developed. However, in almost all cases, the regions and molecules of different resolution are kept fixed and are not in...