Defect configurations and dynamical behavior in a Gay-Berne nematic emulsion

To model a nematic emulsion consisting of a surfactant-coated water droplet dispersed in a nematic host, we performed a molecular dynamics simulation of a droplet immersed in a system of 2048 Gay-Berne ellipsoids in a nematic phase. Strong radial anchoring at the surface of the droplet induced a Saturn ring defect configuration, consistent with theoretical predictions for very small droplets. A surface ring configuration was observed for lower radial anchoring strengths, and a pair of point defects was found near the poles of the droplet for tangential anchoring. We also simulated the falling ball experiment and measured the drag force anisotropy, in the presence of strong radial anchoring as well as zero anchoring strength.Comment: 17 pages, 15 figure

Computer simulations of hard pear-shaped particles

We report results obtained from Monte Carlo simulations investi- gating mesophase formation in two model systems of hard pear-shaped particles. The first model considered is a hard variant of the trun- cated Stone-Expansion model previously shown to form nematic and smectic mesophases when embedded within a 12-6 Gay-Berne-like po- tential [1]. When stripped of its attractive interactions, however, this system is found to lose its liquid crystalline phases. For particles of length to breadth ratio k = 3, glassy behaviour is seen at high pressures, whereas for k = 5 several bi-layer-like domains are seen, with high intradomain order but little interdomain orientational correlation. For the second model, which uses a parametric shape parameter based on the generalised Gay-Berne formalism, results are presented for particles with elongation k = 3; 4 and 5. Here, the systems with k = 3 and 4 fail to display orientationally ordered phases, but that with k = 5 shows isotropic, nematic and, unusually for a hard-particle model, interdigitated smectic A2 phases.</p

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Replication Data for: Resident group size modulates oviposition site selection in Drosophila melanogaster

The data repository contains all raw data associated with the publication, the R-script to process the data and a Python script to proces the videos. Abbreviations in data files: cVA: 11-cis-Vaccenyl Acetate 7-T: (Z)-7-tricosene 9-T: (Z)-9-tricosene 7,11-HD: (7Z,11Z)-heptacosadien