DynamO: a free O(N) general event-driven molecular dynamics simulator.

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo.

Movers and shakers: granular damping in microgravity.

The response of an oscillating granular damper to an initial perturbation is studied using experiments performed in microgravity and granular dynamics simulations. High-speed video and image processing techniques are used to extract experimental data. An inelastic hard sphere model is developed to perform simulations and the results are in excellent agreement with the experiments. In line with previous work, a linear decay of the amplitude is observed. Although this behavior is typical for a friction-damped oscillator, through simulation it is shown that this effect is still present even when friction forces are absent. A simple expression is developed which predicts the optimal damping conditions for a given amplitude and is independent of the oscillation frequency and particle inelasticities.

Structure and stability of helices in square-well homopolymers.

Recently, it has been demonstrated [Magee, Phys. Rev. Lett. 96, 207802 (2006)] that isolated square-well homopolymers can spontaneously break chiral symmetry and "freeze" into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics combined with an optimized parallel tempering scheme to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a "window" of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature; however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.

HFA-134a (1,1,1,2-tetrafluoroethane): effects of inhalation exposure upon reproductive performance, development and maturation of rats.

1. HFA-134a was administered to AHA rats by snout-only inhalation for 1 h daily to assess the effects of treatment on reproduction and development. 2. In a fertility study, rats were exposed to atmospheres of 2500, 10,000 or 50,000 p.p.m. HFA-134a throughout gametogenesis, mating, pregnancy and lactation. 3. In a peri- and post-natal study, rats were exposed to HFA-134a from days 17 to 20 of pregnancy and days 1 to 21 post partum to atmospheres of 1800, 9900 or 64,400 p.p.m. 4. The only treatment-related effect was a slight reduction in body weight gain of males of the treated parental generation at 50,000 p.p.m. (fertility study). 5. In neither study were there any adverse effects of HFA-134a on the reproductive performance of treated animals or on the development, maturation or reproductive performance of up to two successive generations.