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M Karttunen

Publications and source records attributed to M Karttunen.

9 recordsLinked to original sources
PubMed2006

Phase diagram and commensurate-incommensurate transitions in the phase field crystal model with an external pinning potential.

We study the phase diagram and the commensurate-incommensurate transitions in a phase field model of a two-dimensional crystal lattice in the presence of an external pinning potential. The model allows for both elastic and plastic deformations and provides a continuum description of lattice systems, such as for adsorbed atomic layers or two-dimensional vortex lattices. Analytically, a mode expansion analysis is used to determine the ground states and the commensurate-incommensurate transitions in the model as a function of the strength of the pinning potential and the lattice mismatch parameter. Numerical minimization of the corresponding free energy shows reasonable agreement with the analytical predictions and provides details on the topological defects in the transition region. We find that for small mismatch the transition is of first order, and it remains so for the largest values of mismatch studied here. Our results are consistent with results of simulations for atomistic models of adsorbed overlayers.

Journal Article↗
PubMed2006

Cell aggregation: packing soft grains.

Cellular aggregates may be considered as collections of membrane enclosed units with a pressure difference between the internal and external liquid phases. Cells are kept together by membrane adhesion and/or confined space compression. Pattern formation and, in particular, intercellular spacing have important roles in controlling solvent diffusion within such aggregates. A physical approach is used to study generic aspects of cellular packings in a confined space. Average material properties are derived from the free energy. The appearance of penetrating intercellular void channels is found to be critically governed by the cell wall adhesion mechanisms during the formation of dense aggregates. A fully relaxed aggregate efficiently hinders solvent diffusion at high hydrostatic pressures, while a small fraction (approximately 0.1) of adhesion related packing frustration is sufficient for breaking such a blockage even at high a pressure.

Journal Article↗
PubMed2005

Dielectrophoresis of nanocolloids: a molecular dynamics study.

Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature.

Colloids↗
PubMed2004

Anomalously slow phase transitions in self-gravitating systems.

The kinetics of collapse and explosion transitions in microcanonical self-gravitating ensembles is analyzed. A system of point particles interacting via an attractive soft Coulomb potential and confined to a spherical container is considered. We observed that for 100-200 particles collapse takes 10(3) - 10(4) particle crossing times to complete; i.e., it is by two to three orders of magnitude slower than the velocity relaxation. In addition, it is found that the collapse time decreases rapidly with an increase of the soft-core radius. We found that such an anomalously long collapse time is caused by the slow energy exchange between a higher-temperature compact core and relatively cold diluted halo. The rate of energy exchange between the faster modes of the core particles and slower-moving particles of the halo is exponentially small in the ratio of the frequencies of these modes. As the soft-core radius increases and the typical core modes become slower, the ratio of core and halo frequencies decreases and the collapse accelerates. Implications for astrophysical systems and phase transition kinetics are discussed.

Journal Article↗
PubMed2003

Collapses and explosions in self-gravitating systems.

Collapse and explosion (reverse to collapse) transitions in self-gravitating systems are studied by molecular dynamics simulations. A microcanonical ensemble of point particles confined to a spherical box is considered. The particles interact via an attractive soft Coulomb potential. It is observed that a collapse indeed takes place when the energy of the uniform state is set near or below the metastability-instability threshold (collapse energy) as predicted by the mean-field theory. Similarly, an explosion occurs when the energy of the core-halo state is increased above the explosion energy, where according to the mean-field predictions the core-halo state becomes unstable. For systems consisting of 125-500 particles, the collapse takes about 10(5) single-particle crossing times to complete, while a typical explosion is by an order of magnitude faster. A finite lifetime of metastable states is observed. It is also found that the mean-field description of the uniform and core-halo states is exact within the statistical uncertainty of the molecular dynamics data.

Journal Article↗
PubMed2003

Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.8-2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions g(r) of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2000

Towards better integrators for dissipative particle dynamics simulations

Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient. We assess the quality of these integration schemes, including variants based on a recently suggested self-consistent approach, and examine their relative performance. Implications of integrator-induced effects are discussed.

Journal Article↗