17 research outputs found
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