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Biomedical subjects

I Vattulainen

Publications and source records attributed to I Vattulainen.

6 recordsLinked to original sources
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↗
PubMed1999

Framework for testing random numbers in parallel calculations.

We propose a framework for testing the quality of random numbers in parallel calculations. The key idea is to study cross-correlations between distinct sequences of random numbers via correlations between various diffusing random walkers, each of which is governed by a distinct random number sequence. The asymptotic power-law behavior of the corresponding correlation functions yields exponents, which can be compared with exact theoretical results. Correlations prior to the asymptotic regime can be further investigated by other complementary methods. We demonstrate this approach by three efficient tests, which find correlations in various commonly used pseudorandom number generators. Finally, we discuss some ideas for applying this framework in other contexts.

Journal Article↗