Contracts and Behavioral Patterns for SoS: The EU IP DANSE approach

This paper presents some of the results of the first year of DANSE, one of the first EU IP projects dedicated to SoS. Concretely, we offer a tool chain that allows to specify SoS and SoS requirements at high level, and analyse them using powerful toolsets coming from the formal verification area. At the high level, we use UPDM, the system model provided by the british army as well as a new type of contract based on behavioral patterns. At low level, we rely on a powerful simulation toolset combined with recent advances from the area of statistical model checking. The approach has been applied to a case study developed at EADS Innovation Works.Comment: In Proceedings AiSoS 2013, arXiv:1311.319

Attraction and ionic correlations between charged stiff polyelectrolytes

We use Molecular Dynamics simulations to study attractive interactions and the underlying ionic correlations between parallel like-charged rods in the absence of additional salt. For a generic bulk system of rods we identify a reduction of short range repulsions as the origin of a negative osmotic coefficient. The counterions show signs of a weak three-dimensional order in the attractive regime only once the rod-imposed charge-inhomogeneities are divided out. We also treat the case of attraction between a single pair of rods for a few selected line charge densities and rod radii. Measurements of the individual contributions to the force between close rods are studied as a function of Bjerrum length. We find that even though the total force is always attractive at sufficiently high Bjerrum length, the electrostatic contribution can ultimately become repulsive. We also measure azimuthal and longitudinal correlation functions to answer the question how condensed ions are distributed with respect to each other and to the neighboring rod. For instance, we show that the prevalent image of mutually interlocked ions is qualitatively correct, even though modifications due to thermal fluctuations are usually strong.Comment: 14 pages, 14 figures, REVTeX4 styl

Electrostatics in Periodic Slab Geometries I

We propose a new method to sum up electrostatic interactions in 2D slab geometries. It consists of a combination of two recently proposed methods, the 3D Ewald variant of Yeh and Berkowitz, J. Chem. Phys. 111 (1999) 3155, and the purely 2D method MMM2D by Arnold and Holm, to appear in Chem. Phys. Lett. 2002. The basic idea involves two steps. First we use a three dimensional summation method whose summation order is changed to sum up the interactions in a slab-wise fashion. Second we subtract the unwanted interactions with the replicated layers analytically. The resulting method has full control over the introduced errors. The time to evaluate the layer correction term scales linearly with the number of charges, so that the full method scales like an ordinary 3D Ewald method, with an almost linear scaling in a mesh based implementation. In this paper we will introduce the basic ideas, derive the layer correction term and numerically verify our analytical results.Comment: 10 pages, 7 figure

Electrostatics in Periodic Slab Geometries II

In a previous paper a method was developed to subtract the interactions due to periodically replicated charges (or other long-range entities) in one spatial dimension. The method constitutes a generalized "electrostatic layer correction" (ELC) which adapts any standard 3D summation method to slab-like conditions. Here the implementation of the layer correction is considered in detail for the standard Ewald (EW3DLC) and the PPPM mesh Ewald (PPPMLC) methods. In particular this method offers a strong control on the accuracy and an improved computational complexity of O(N log N) for mesh-based implementations. We derive anisotropic Ewald error formulas and give some fundamental guidelines for optimization. A demonstration of the accuracy, error formulas and computation times for typical systems is also presented.Comment: 14 pages, 7 figure

Attraction and unbinding of like-charged rods

We investigate the effective interaction between two like-charged rods in the regime of large electrostatic coupling parameters using both Molecular Dynamics simulation techniques and the recently introduced strong-coupling theory. We obtain attraction between the rods for elevated Manning parameters accompanied by an equilibrium surface-to-surface separation of the order of the Gouy-Chapman length. A continuous unbinding between the rods is predicted at a threshold Manning parameter of 2/3.Comment: 8 pages, 2 figure