Discontinuous Molecular Dynamics for Rigid Bodies: Applications

Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 2 to 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. Qualitative differences in the dynamics of the two models are related to the relatively crude treatment of variations in the repulsive interactions as one benzene molecule rotates by another.Comment: 14 pages, double column revte

Discontinuous Molecular Dynamics for Semi-Flexible and Rigid Bodies

A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and interaction rules are derived from Lagrangian mechanics in the presence of constraints. This approach is most suitable when the body is composed of relatively few point masses or is semi-flexible. In the second method, the equations of rigid bodies are used to derive explicit analytical expressions for the free evolution of arbitrary rigid molecules and to construct a simple scheme for computing interaction rules. Efficient algorithms for the search for the times of interaction events are designed in this context, and the handling of missed interaction events is discussed.Comment: 16 pages, double column revte

University of Guelph, 2000 Ottawa :National Library of Canada

In this work, we examine some of the properties of a model Langmuir monolayer, which consists of surfactant molecules (amphiphillic organic molecules) deposited onto a water subphase. The surfactants are modeled as rigid rods composed of a head and tail segment. The tails consist of 'nt' ≈ 4-7 effective monomers representing CH2 methylene groups. These rigid rods interact via site-site Lennard-Jones potentials with different interaction parameters for the tail-tail, head-tail and head-head interactions. The present research has focused on some of the key physical parameters, such as chain length, bond length, and head diameter, responsible for driving tilting transitions from uniformly tilted to untilted phases and between different tilt-ordered phases. At zero temperature, by systematically increasing the head-tail diameter ratio and bond length, we have observed continuous transitions from untilted to tilted phases and first-order transitions from next-nearest-neighbor (NNN) to nearest-neighbor (NN) tilted phases. Some metastable phases have also been discovered where coexistence occurs between molecules with the same kind of tilt ordering. To investigate system properties at finite temperature, we performed Monte Carlo simulations in the constant molecular number N, area A, and temperature T (NAT) ensemble. Some of the earlier studies incorporated a continuum model to characterize the water subphase, but this led to unphysical results. Subsequent work, where the water was replaced by a hard surface, examined the effects on the tilting transition temperature 'T c' due to variations in density, chain length and head-tail diameter mismatch. In some recent studies, we have utilized a more realistic model for the surfactant-water interactions, developed by Karaborni and Toxvaerd, in order to re-examine the role which the water subphase has on tilt-ordering

Physical Review E 6305 5 056701 056701 AMERICAN PHYSICAL SOC COLLEGE PK; ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA

In this paper various extensions of the parallel-tempering algorithm are developed and their properties are analyzed. The algorithms are designed to alleviate quasiergodic sampling in systems which have rough energy landscapes by coupling individual Monte Carlo chains to form a composite chain. As with parallel tempering, the procedures are based upon extending the state space to include parameters to encourage sampling mobility. One of the drawbacks of the parallel-tempering method is the stochastic nature of the Monte Carlo dynamics in the auxiliary variables which extend the state spate. In this work. the possibility of improving the sampling rate by designing deterministic methods of moving through the parameter space is investigated. The methods developed in this article, which are based upon a statistical quenching and heating procedure similar in spirit to simulated annealing, are tested on a simple two-dimensional spin system (xy model) and on a model in vacuo polypeptide system. In the coupled Monte Carlo chain algorithms, we find that the net mobility of the composite chain is determined by the competition between the characteristic time of coupling between adjacent chains and the degree of overlap of their distributions. Extensive studies of all methods are carried out to obtain optimal sampling conditions. In particular, the most efficient parallel-tempering procedure is to attempt to swap configurations after very few Monte Carlo updates of the composite chains. Furthermore, it is demonstrated that, contrary to expectations, the deterministic procedure does not improve the sampling rate over that of parallel tempering

Home range and habitat selection of a reintroduced African wild dog (Lycaon pictus) pack in a small South African game reserve

The African wild dog (Lycaon pictus) is an endangered species and South Africa has only one remaining viable population. Reintroduction of this species in South Africa is of high conservation priority and knowledge of the species' ecology is crucial for success. In this study, important information was gained regarding the reintroduction process although it ultimately failed. The current conservation plan for wild dogs incorporates such existing knowledge, but results from reintroductions (including failures) are needed to strengthen the strategy and its success. The main purpose of this study was to quantify home range area and habitat selection patterns of a wild dog pack unsuccessfully reintroduced into Mkhuze Game Reserve (MGR). A total of 847 radio-tracking fixes of the pack were collected. The home range area of the pack was estimated to be 383.9 km2 (100% minimum convex polygon method) or 377.9 km2 (95% fixed-kernel method), each value being larger than the area of the game reserve (360 km2). Significant monthly variations in home range areas of the pack were detected, with a maximum monthly home range area reached at ~10 months after tracking began (19 months after the pack was reintroduced). Independent of season, the pack consistently selected Acacia nilotica low-closed woodland and consistently avoided riverine forest habitats. Small differences in home range areas of the pack were found between wet and dry seasons. The deaths of some wild dogs were the result of snares, and others may have been due to predation or hunting injuries. We present evidence that factors including game reserve area, availability of preferred habitat and climate may have contributed to the distribution patterns and ultimately the failure to maintain viable numbers during this wild dog reintroduction. The reintroduction of wild dogs to MGR was successful in that the introduced wild dogs bred, owing to the release of a pregnant female, but was considered unsuccessful since none of the dogs from the reintroduced pack survived or remained in MGR for more than two years. However, two wild dogs returned shortly after radio-tracking sessions ceased and were soon joined by another female from an adjacent game reserve