A5011413105- Nanopore and Nanochannel Transport Studies
- Protein Structure and Dynamics
- Spectroscopy and Quantum Chemical Studies
- Material Dynamics and Properties
- Block Copolymer Self-Assembly
- Theoretical and Computational Physics
- Numerical methods for differential equations
- Rheology and Fluid Dynamics Studies
- Electrostatics and Colloid Interactions
- Advanced NMR Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Lattice Boltzmann Simulation Studies
- Particle accelerators and beam dynamics
- Advanced Mathematical Modeling in Engineering
- Machine Learning in Materials Science
- Advanced Physical and Chemical Molecular Interactions
- Liquid Crystal Research Advancements
- Advanced Thermodynamics and Statistical Mechanics
- Advanced Numerical Methods in Computational Mathematics
- Carbon Nanotubes in Composites
- Advanced Materials and Mechanics
- Advanced Chemical Physics Studies
- Characterization and Applications of Magnetic Nanoparticles
- Underwater Acoustics Research
- Granular flow and fluidized beds
National Institute of Chemistry
2016-2025
University of Ljubljana
2014-2025
Partnership for Advanced Computing in Europe
2021
Institute of Mathematics, Physics, and Mechanics
2016
University of Groningen
2014
Max Planck Institute for Polymer Research
2005-2013
University of Bologna
2013
ETH Zurich
2010
Max Planck Society
2006-2009
We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics simulations. The presented approach is tailor-made molecular systems where atomistic required only in spatially localized domains whereas lower mesoscopic level of detail sufficient the rest system. Our method allows an on-the-fly interchange between given molecule’s atomic and coarse-grained levels description, enabling us to reach large length time scales while retaining details tested...
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving equilibrium with surrounding introduce conceptual problems thermodynamic consistency. In this work we present general scheme based on arguments which ensures among molecules different representation. The robustness algorithm is tested for two examples, namely an adaptive resolution simulation, atomistic/coarse-grained, liquid tetrahedral and binary mixture spherical solutes.
Typical experimental setups for molecular systems must deal with a certain coupling to the external environment, that is, system is open and exchanges mass, momentum, energy its surroundings. Instead, standard simulations are mostly performed using periodic boundary conditions constant number of molecules. In this review, we summarize major development simulation methodologies, which, contrary techniques, up boundaries allow exchange matter in out equilibrium. particular, construct review...
Vibrational spectroscopy studies show that the bulk water bending band becomes narrower with increasing temperature (Maréchal, Y. J. Mol. Struct. 1994, 322, 105). Since this counterintuitive effect is not associated quantum nature of nuclear motion a molecular dynamics (MD) simulation expected to reproduce it even in classical limit. We have performed MD flexible simple point charge (SPC) and extended SPC (SPC/E) models determine dependence vibrational spectrum. The intramolecular potential...
We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties molecular fluids. The standard DPD acts only on relative velocity along interatomic axis. Our extension includes damping perpendicular components velocity, whilst keeping advantages conserving Galilei invariance and within our error bar also hydrodynamics. This leads to second friction parameter tuning system. Numerical simulations simple Lennard-Jones fluid liquid...
The adaptive resolution scheme (AdResS) for efficient hybrid particle-based atomistic/mesoscale molecular dynamics (MD) simulations recently introduced by us, [J. Chem. Phys. 123, 224106 (2005)] is extended to high density liquids with spherical boundaries between the atomistic and mesoscale regions. key feature of this approach that it allows a dynamical change number degrees freedom during course MD simulation an on-the-fly switching mesoscopic levels detail. Pressure variations occurring...
Water plays a central role in biological systems and processes, is equally relevant large range of industrial technological applications. Being the most important natural solvent, its presence uniquely influences function as well technical processes. Because their importance, aqueous solutions are among experimentally theoretically studied systems. However, many questions still remain open. Both experiments theoretical models usually restricted to specific cases. In particular all-atom...
We present a triple-scale simulation of molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions liquid are concurrently coupled. The presented multiscale approach, covers length scales ranging from micro- to macroscale, is combination two dual-scale models: particle-based adaptive resolution scheme (AdResS), couples atomic mesoscopic scales, hybrid continuum-molecular dynamics (HybridMD). combined AdResS-HybridMD successfully sorts out problem large molecule...
We present an adaptive resolution simulation of protein G in multiscale water. couple atomistic water around the with mesoscopic water, where four molecules are represented one coarse-grained bead, farther away. circumvent difficulties that arise from coupling to model via a 4-to-1 molecule coarse-grain mapping by using bundled models, i.e., we restrict relative movement mapped same bead employing harmonic springs. The change their particle and vice versa adaptively on-the-fly. Having...
The new symplectic molecular dynamics (MD) integrators presented in the first paper of this series were applied to perform MD simulations water. physical properties a system flexible TIP3P water molecules computed by integrators, such as diffusion coefficients, orientation correlation times, and infrared (IR) spectra, are good agreement with results obtained standard method. comparison between integrators' method's integration time step sizes indicates that resulting algorithm allows 3.0 fs...
We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., liquid tetrahedral molecules, is represented within certain radius from the polymer's center mass with high level detail, while lower coarse-grained used for more distant solvent. sphere moves and freely exchanges molecules low region through transition regime. solvent change their number degrees freedom on-the-fly. show that our approach correctly reproduces static...
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive resolution procedure allows for changing from coarse-grained to an all-atom representation and vice versa on-the-fly. In order find the most appropriate model be employed with AdResS, we first study accuracy different models in reproducing structural properties system. Typically, have higher diffusion constant than...
We describe a web tool ENZO (Enzyme Kinetics), graphical interface for building kinetic models of enzyme catalyzed reactions. automatically generates the corresponding differential equations from stipulated reaction scheme. These are processed by numerical solver and regression algorithm which fits coefficients to experimentally observed time course curves. allows rapid evaluation rival schemes can be used routine tests in kinetics. It is freely available as tool, at http://enzo.cmm.ki.si.
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms special purpose hardware, accessing time scales necessary to capture structural biomolecules remains a daunting task. In this work, we present novel framework advance simulation by up 3 orders magnitude learning effective dynamics (LED) LED augments equation-free methodology employing probabilistic mapping between coarse fine using mixture density network...
New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of vibrations to solve Hamiltonian equations motion. The presented analytically resolve internal high-frequency introducing a translating and rotating coordinate system molecule calculating normal modes an isolated only. translation rotation are treated as vibrational motions frequency zero. All types motion thus described in terms coordinates. method's time reversibility...
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models the liquid. The presented hydrodynamic solver for molecular liquids enables insertion large molecules into atomistic domain through mesoscopic region. show that scheme is robust against details model owing to conservation linear momentum adaptive resolution forces. Our multiscale approach designed simulations open domains with relatively molecules, either in grand...
We present adaptive resolution molecular dynamics simulations of aqueous and apolar solvents using coarse-grained models that are compatible with the MARTINI force field. As representatives both classes we have chosen liquid water butane, respectively, at ambient temperature. The solvent molecules change their back forth between atomistic representations according to positions in system. difficulties arise from coupling a model multimolecule mapping, for example, 4-to-1 mapping case Simple...
We present a multiscale simulation of DNA molecule in 1 M NaCl salt solution environment, employing the adaptive resolution approach that allows solvent molecules, i.e., water and ions, to change their from atomistic coarse-grained vice versa adaptively on-the-fly. The region high moves together with center-of-mass so itself is always modeled at resolution. show our simulations yield stable DNA-solution system, statistical properties similar those produced by conventional all-atom molecular...
Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect conventional atomistic simulations. For these kind of simulations, it is essential develop accurate multiscale water models that can be used solvate biophysical systems interest. Recently, a 4-to-1 mapping was couple the bundled-simple point charge MARTINI model. Here, we extend supramolecular coarse-grained explicit charges. In...
Shearing polymer melts at constant normal pressure produces different rheology than shearing a volume, as revealed by AdResS-enabled open boundary MD simulations of star melts.
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model or far too small time scales. To overcome this problem multiscale techniques are being developed. However, in almost all cases, regions molecules different resolution kept fixed not equilibrium with each other. We here give a basic theoretical framework for an efficient flexible coupling regimes. The approach leads concept, which can be seen as geometry-induced...