Mej Mikko Karttunen

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.

Electrorotation in graded colloidal suspensions

Biological cells can be treated as composites of graded material inclusions. In addition to biomaterials, graded composites are important in more traditional materials science. In this paper, we investigate the electrorotation spectrum of a graded colloidal suspension in an attempt to discuss its dielectric properties. For that, we use the recently obtained differential effective dipole approximation and generalize it for nonspherical particles. We find that variations in the conductivity profile may make the characteristic frequency redshifted and have also an effect on the rotation peak. On the other hand, variations in the dielectric profile may enhance the rotation peak, but do not have any significant effect on the characteristic frequency. In the end, we apply our theory to fit experimental data obtained for yeast cells and find good agreement.

The good, the bad and the user in soft matter simulations

Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

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.

Dielectrophoresis of charged colloidal suspensions.

We present a theoretical study of dielectrophoretic (DEP) crossover spectrum of two polarizable particles under the action of a nonuniform ac electric field. For two approaching particles, the mutual polarization interaction yields a change in their respective dipole moments, and hence, in the DEP crossover spectrum. The induced polarization effects are captured by the multiple image method. Using spectral representation theory, an analytic expression for the DEP force is derived. We find that the mutual polarization effects can change the crossover frequency at which the DEP force changes sign. The results are found to be in agreement with recent experimental observation and as they go beyond the standard theory, they help to clarify the important question of the underlying polarization mechanisms.

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.

Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: Effects of multipolar interactions

We present a theory to investigate electrokinetic behavior, namely, electrorotation and dielectrophoresis under alternating current (ac) applied fields for a pair of touching inhomogeneous colloidal particles and biological cells. These inhomogeneous particles are treated as graded ones with physically motivated model dielectric and conductivity profiles. The mutual polarization interaction between the particles yields a change in their respective dipole moments, and hence in the ac electrokinetic spectra. The multipolar interactions between polarized particles are accurately captured by the multiple images method. In the point-dipole limit, our theory reproduces the known results. We find that the multipolar interactions as well as the spatial fluctuations inside the particles can affect the ac electrokinetic spectra significantly.

Spectral representation of the effective dielectric constant of graded composites

We generalize the Bergman-Milton spectral representation, originally derived for a two-component composite, to extract the spectral density function for the effective dielectric constant of a graded composite. This work has been motivated by a recent study of the optical absorption spectrum of a graded metallic film [Huang and Yu, Appl. Phys. Lett. 85, 94 (2004)] in which a broad surface-plasmon absorption band was shown to be responsible for enhanced nonlinear optical response and an attractive figure of merit. It turns out that, unlike in the case of homogeneous constituent components, the characteristic function of a graded composite is a continuous function because of the continuous variation of the dielectric function within the constituent components. Analytical generalization to three-dimensional graded composites is discussed, and numerical calculations for multilayer composites are given as a simple application.

Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity.

We used the crystal structure of prolyl oligopeptidase (POP) with bound Z-pro-prolinal (ZPP) inhibitor (Protein Data Bank (PDB) structure 1QFS) to perform an intensive molecular dynamics study of the POP-ZPP complex. We performed 100 ns of simulation with the hemiacetal bond, through which the ZPP is bound to the POP, removed in order to better investigate the binding cavity environment. From basic analysis, measuring the radius of gyration, root mean square deviation, solvent accessible surface area and definition of the secondary structure of protein, we determined that the protein structure is highly stable and maintains its structure over the entire simulation time. This demonstrates that such long time simulations can be performed without the protein structure losing stability. We found that water bridges and hydrogen bonds play a negligible role in binding the ZPP thus indicating the importance of the hemiacetal bond. The two domains of the protein are bound by a set of approximately 12 hydrogen bonds, specific to the particular POP protein.

Nonlinear driven response of a phase-field crystal in a periodic pinning potential.

We study numerically the phase diagram and the response under a driving force of the phase field crystal model for pinned lattice systems introduced recently for both one- and two-dimensional systems. The model describes the lattice system as a continuous density field in the presence of a periodic pinning potential, allowing for both elastic and plastic deformations of the lattice. We first present results for phase diagrams of the model in the absence of a driving force. The nonlinear response to a driving force on an initially pinned commensurate phase is then studied via overdamped dynamic equations of motion for different values of mismatch and pinning strengths. For large pinning strength the driven depinning transitions are continuous, and the sliding velocity varies with the force from the threshold with power-law exponents in agreement with analytical predictions. Transverse depinning transitions in the moving state are also found in two dimensions. Surprisingly, for sufficiently weak pinning potential we find a discontinuous depinning transition with hysteresis even in one dimension under overdamped dynamics. We also characterize structural changes of the system in some detail close to the depinning transition.