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Florian Müller-Plathe

Publications and source records attributed to Florian Müller-Plathe.

10 recordsLinked to original sources
PubMed2005

Reverse nonequilibrium molecular-dynamics calculation of the Soret coefficient in liquid benzene/cyclohexane mixtures.

Reverse nonequilibrium molecular dynamics is the method applied here for the investigation of thermal diffusion in realistic molecular fluids. The Soret coefficients of benzene/cyclohexane mixtures are calculated using an all-atom model. The autocorrelation functions indicate that the mole fraction gradient converges much slower than the temperature gradient. Compared to experimental data, the results show the same tendency of the Soret coefficient variation versus the mole fraction. Although a systematic error exists for the magnitude of the Soret coefficient, a meanwhile systematic error for both the mutual diffusion and thermal diffusion coefficients provides some explanation of it; and the calculation with different force field parameters indicates a possibility to annihilate the systematic error. The influences of algorithm variables such as cutoff lengths and perturbation intensities are tested. Furthermore the temperature dependence of the Soret effect is observed, yielding the same trend as previous studies.

Journal Article↗
PubMed2005

Molecular dynamics simulation of water near nanostructured hydrophobic surfaces: interfacial energies.

We present results from molecular dynamics simulations of water near structured hydrophobic surfaces. The surface structures reported herein are a planar alkane crystal as a reference and crystals with a hole and a protrusion of approximately 2.5 nm diameter and 0.5 nm depth or height. All indicators show that surface structuring increases the hydrophobicity: The water density is reduced near the structure elements, and the number of residual contacts between water and the surface decreases by about 40 % with respect to the planar surface. Thermodynamic integration shows that the interfacial energy of the structured surfaces is about 7 mJ m(-2) higher for structured surfaces than for the planar surface. The hydrophobicity increases by a similar amount for the hole and the protrusion geometries compared to the planar surface.

Alkanes↗
PubMed2005

The hydrophobicity of nanostructured alkane and perfluoro alkane surfaces: a comparison by molecular dynamics simulation.

In this contribution we investigate the differences in the hydrophobicity of a perfluoro-n-eicosane crystal and the n-eicosane crystal by molecular dynamics simulation. The results were analysed in terms of density of water at the interface, the chemical potential of water at the interface and the orientational ordering of water at the interface. The perfluoro-n-eicosane crystal-water interface is found to have a less density, higher chemical potential and a weaker orientational ordering at the interface than the corresponding n-eicosane crystal.

Journal Article↗
PubMed2005

Effect of nanostructure on the properties of water at the water-hydrophobic interface: a molecular dynamics simulation.

The local structure of water near hydrophobic surfaces of different surface topographies has been analyzed by molecular dynamics simulation. An alkane crystal has been taken as the parent model for a hydrophobic surface. Surface structures were created by placing pits into it, which were half a nanometer deep and several nanometers wide. Around all structures, the water has a lower density, less orientational ordering, fewer water-water hydrogen bonds, and fewer surface contacts than for a flat unstructured surface. This indicates that the structured surfaces are more hydrophobic than the flat surface. Of the structures investigated, pits with a diameter of approximately 2.5 nm were effective in increasing the hydrophobic character of the surface.

Journal Article↗
PubMed2005

A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise.

We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81 W m(-1) K(-1). It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system.

Journal Article↗
PubMed2003

Deriving effective mesoscale potentials from atomistic simulations.

We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes.

Journal Article↗
PubMed2002

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back.

Polymers can be theoretically and computationally described by models pertaining to different length scales and corresponding time scales. These models have traditionally been used independently of each other. Recently, considerable progress has been made in systematically linking models of different scales. This Review focuses on the generation of lattice and off-lattice coarse-grained polymer models, whose "monomers" correspond to roughly a chemical repeat unit, from chemically detailed atomistic simulations of the same polymers. Computational methods are described as well as applications to polymers in the melt and in solution. The success of multiscale simulations in solving real-world polymer problems that could not be solved in any other way suggests that they will have an important role to play in the future.

Biopolymers↗
PubMedDate not supplied

Parallelizing a molecular dynamics algorithm on a multiprocessor workstation using OpenMP.

The atomistic molecular dynamics program YASP has been parallelized for shared-memory computer architectures. Parallelization was restricted to the most CPU-time-consuming parts: neighbor-list construction, calculation of nonbonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbor list did the data structure have to be changed. The parallel code achieves a useful speedup over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on the characteristics of the simulated systems. On dual-processor Xeon systems, the speedup is about 1.7.

Journal Article↗