Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, v... more Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and employed for the simulation of electrolytes in aqueous solution. The enzymatically catalysed hydroxylation of oleic acid is investigated by molecular dynamics simulation taking the internal degrees of freedom of the macromolecules into account. Thereby, Ewald summation methods are used to compute the long range electrostatic interactions. In systems with a phase boundary, the dispersive interaction, which is modelled by the Lennard-Jones potential here, has a more significant long range contribution than in homogeneous systems. This effect is accounted for by implementing the Janecek cutoff correction scheme. On this basis, the HPC infrastructure at the Steinbuch Centre for Computing was accessed and efficiently used, yielding new insights on the molecular systems under consideration.
Interfacial phenomena play an important role in many engineering applications such as evaporation... more Interfacial phenomena play an important role in many engineering applications such as evaporation, coating technology and mass transfer. Especially in microscale systems like porous media, these effects dominate the behavior of the entire system. On the molecular length scale, finite size effects significantly influence the properties of an interface, such as its interfacial tension. The interfacial tension of a droplet depends on its size. According to the Tolman approach, the interfacial tension of an nanodroplet deviates from that of a planar interface due to its extremely curved shape [1]. Recent results claim that an additional term of 1/R³ is needed to consider both the change in curvature and size [2]. As a curvature independent study of the size effect, vapor-liquid simulations with planar interfaces and varied thickness of the liquid film are carried out. MD runs are conducted with successively thinner films, until a minimum stable thickness is reached for the given tempera...
Physica A: Statistical Mechanics and its Applications, 2013
ABSTRACT One of the long standing challenges in molecular simulation is the description of interf... more ABSTRACT One of the long standing challenges in molecular simulation is the description of interfaces. On the molecular length scale, finite size effects significantly influence the properties of the interface such as its interfacial tension, which can be reliably investigated by molecular dynamics simulation of planar vapor-liquid interfaces. For the Lennard-Jones fluid, finite size effects are examined here by varying the thickness of the liquid slab. It is found that the surface tension and density in the center of the liquid region decreases significantly for thin slabs. The influence of the slab thickness on both the liquid density and the surface tension is found to scale with 1/S^3 in terms of the slab thickness S, and a linear correlation between both effects is obtained. The results corroborate the analysis of Malijevsk\'y and Jackson, J. Phys.: Cond. Mat. 24: 464121 (2012), who recently detected an analogous effect for the surface tension of liquid nanodroplets.
ABSTRACT A slab based long range correction approach for multi-site Lennard-Jones models is prese... more ABSTRACT A slab based long range correction approach for multi-site Lennard-Jones models is presented for systems with a planar film geometry that is based on the work by Janecek, J. Phys. Chem. B 110: 6264 (2006). It is efficient because it relies on a center-of-mass cutoff scheme and scales in terms of numerics almost perfectly with the molecule number. For validation, a series of simulations with the two-center Lennard-Jones model fluid, carbon dioxide and cyclohexane is carried out. The results of the present approach, a site-based long range correction and simulations without any long range correction are compared with respect to the saturated liquid density and the surface tension. The present simulation results exhibit only a weak dependence on the cutoff radius, indicating a high accuracy of the implemented long range correction.
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, v... more Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and employed for the simulation of electrolytes in aqueous solution. The enzymatically catalysed hydroxylation of oleic acid is investigated by molecular dynamics simulation taking the internal degrees of freedom of the macromolecules into account. Thereby, Ewald summation methods are used to compute the long range electrostatic interactions. In systems with a phase boundary, the dispersive interaction, which is modelled by the Lennard-Jones potential here, has a more significant long range contribution than in homogeneous systems. This effect is accounted for by implementing the Janecek cutoff correction scheme. On this basis, the HPC infrastructure at the Steinbuch Centre for Computing was accessed and efficiently used, yielding new insights on the molecular systems under consideration.
Interfacial phenomena play an important role in many engineering applications such as evaporation... more Interfacial phenomena play an important role in many engineering applications such as evaporation, coating technology and mass transfer. Especially in microscale systems like porous media, these effects dominate the behavior of the entire system. On the molecular length scale, finite size effects significantly influence the properties of an interface, such as its interfacial tension. The interfacial tension of a droplet depends on its size. According to the Tolman approach, the interfacial tension of an nanodroplet deviates from that of a planar interface due to its extremely curved shape [1]. Recent results claim that an additional term of 1/R³ is needed to consider both the change in curvature and size [2]. As a curvature independent study of the size effect, vapor-liquid simulations with planar interfaces and varied thickness of the liquid film are carried out. MD runs are conducted with successively thinner films, until a minimum stable thickness is reached for the given tempera...
Physica A: Statistical Mechanics and its Applications, 2013
ABSTRACT One of the long standing challenges in molecular simulation is the description of interf... more ABSTRACT One of the long standing challenges in molecular simulation is the description of interfaces. On the molecular length scale, finite size effects significantly influence the properties of the interface such as its interfacial tension, which can be reliably investigated by molecular dynamics simulation of planar vapor-liquid interfaces. For the Lennard-Jones fluid, finite size effects are examined here by varying the thickness of the liquid slab. It is found that the surface tension and density in the center of the liquid region decreases significantly for thin slabs. The influence of the slab thickness on both the liquid density and the surface tension is found to scale with 1/S^3 in terms of the slab thickness S, and a linear correlation between both effects is obtained. The results corroborate the analysis of Malijevsk\'y and Jackson, J. Phys.: Cond. Mat. 24: 464121 (2012), who recently detected an analogous effect for the surface tension of liquid nanodroplets.
ABSTRACT A slab based long range correction approach for multi-site Lennard-Jones models is prese... more ABSTRACT A slab based long range correction approach for multi-site Lennard-Jones models is presented for systems with a planar film geometry that is based on the work by Janecek, J. Phys. Chem. B 110: 6264 (2006). It is efficient because it relies on a center-of-mass cutoff scheme and scales in terms of numerics almost perfectly with the molecule number. For validation, a series of simulations with the two-center Lennard-Jones model fluid, carbon dioxide and cyclohexane is carried out. The results of the present approach, a site-based long range correction and simulations without any long range correction are compared with respect to the saturated liquid density and the surface tension. The present simulation results exhibit only a weak dependence on the cutoff radius, indicating a high accuracy of the implemented long range correction.
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