Kinetics of phase transformations in a model with metastable fluid-fluid separation: A molecular dynamics study

By molecular dynamics (MD) simulations we study the crystallization process in a model system whose particles interact by a spherical pair potential with a narrow and deep attractive well adjacent to a hard repulsive core. The phase diagram of the model displays a solid-fluid equilibrium, with a metastable fluid-fluid separation. Our computations are restricted to fairly small systems (from 2592 to 10368 particles) and cover long simulation times, with constant energy trajectories extending up to 76x10(6) MD steps. By progressively reducing the system temperature below the solid-fluid line, we first observe the metastable fluid-fluid separation, occurring readily and almost reversibly upon crossing the corresponding line in the phase diagram. The nucleation of the crystal phase takes place when the system is in the two-fluid metastable region. Analysis of the temperature dependence of the nucleation time allows us to estimate directly the nucleation free energy barrier. The results are compared with the predictions of classical nucleation theory. The critical nucleus is identified, and its structure is found to be predominantly fcc. Following nucleation, the solid phase grows steadily across the system, incorporating a large number of localized and extended defects. We discuss the relaxation processes taking place both during and after the crystallization stage. The relevance of our simulation for the kinetics of protein crystallization under normal experimental conditions is discussed. (C) 2002 American Institute of Physics.

A new look at the pulsating DB white dwarf GD 358: Line-of-sight velocity measurements and constraints on model atmospheres

We report on our findings of the bright, pulsating, helium atmosphere white dwarf GD 358, based on time-resolved optical spectrophotometry. We identify 5 real pulsation modes and at least 6 combination modes at frequencies consistent with those found in previous observations. The measured Doppler shifts from our spectra show variations with amplitudes of up to 5.5 km s-1 at the frequencies inferred from the flux variations. We conclude that these are variations in the line-of-sight velocities associated with the pulsational motion. We use the observed flux and velocity amplitudes and phases to test theoretical predictions within the convective driving framework, and compare these with similar observations of the hydrogen atmosphere white dwarf pulsators (DAVs). The wavelength dependence of the fractional pulsation amplitudes (chromatic amplitudes) allows us to conclude that all five real modes share the same spherical degree, most likely, l=1. This is consistent with previous identifications based solely on photometry. We find that a high signal-to-noise mean spectrum on its own is not enough to determine the atmospheric parameters and that there are small but significant discrepancies between the observations and model atmospheres. The source of these remains to be identified. While we infer Teff =24 kK and log g ~ 8.0 from the mean spectrum, the chromatic amplitudes, which are a measure of the derivative of the flux with respect to the temperature, unambiguously favour a higher effective temperature, 27 kK, which is more in line with independent determinations from ultra-violet spectra.

Relative energetics and structural properties of zirconia using a self-consistent tight-binding model

We describe an empirical, self-consistent, orthogonal tight-binding model for zirconia, which allows for the polarizability of the anions at dipole and quadrupole levels and for crystal field splitting of the cation d orbitals, This is achieved by mixing the orbitals of different symmetry on a site with coupling coefficients driven by the Coulomb potentials up to octapole level. The additional forces on atoms due to the self-consistency and polarizabilities are exactly obtained by straightforward electrostatics, by analogy with the Hellmann-Feynman theorem as applied in first-principles calculations. The model correctly orders the zero temperature energies of all zirconia polymorphs. The Zr-O matrix elements of the Hamiltonian, which measure covalency, make a greater contribution than the polarizability to the energy differences between phases. Results for elastic constants of the cubic and tetragonal phases and phonon frequencies of the cubic phase are also presented and compared with some experimental data and first-principles calculations. We suggest that the model will be useful for studying finite temperature effects by means of molecular dynamics.

Towards agent-oriented model-driven architecture

Model Driven Architecture supports the transformation from reusable models to executable software. Business representations, however, cannot be fully and explicitly represented in such models for direct transformation into running systems. Thus, once business needs change, the language abstractions used by MDA (e.g. Object Constraint Language / Action Semantics), being low level, have to be edited directly. We therefore describe an Agent-oriented Model Driven Architecture (AMDA) that uses a set of business models under continuous maintenance by business people, reflecting the current business needs and being associated with adaptive agents that interpret the captured knowledge to behave dynamically. Three contributions of the AMDA approach are identified: 1) to Agent-oriented Software Engineering, a method of building adaptive Multi-Agent Systems; 2) to MDA, a means of abstracting high level business-oriented models to align executable systems with their requirements at runtime; 3) to distributed systems, the interoperability of disparate components and services via the agent abstraction.

An exploratory non-LTE model atmosphere analysis of B-type supergiants in the Small Magellanic Cloud

A preliminary differential non-LTE model atmosphere analysis of moderate resolution (R ~ 5 000) and signal-to-noise ratio spectra of 48 Small Magellanic Cloud B-type supergiants is presented. Standard techniques are adopted, viz. plane-parallel geometry and radiative and hydrostatic equilibrium. Spectroscopic atmospheric parameters (T_eff, log g and v_turb), luminosities and chemical abundances (He, C, N, O, Mg and Si) are estimated. These are compared with those deduced for a comparable sample of Galactic supergiants. The SMC targets appear to have similar atmospheric parameters, luminosities and helium abundances to the Galactic sample. Their magnesium and silicon underabundances are compatible with those found for main sequence SMC objects and there is no evidence for any large variation in their oxygen abundances. By contrast both their carbon and nitrogen lines strengths are inconsistent with single abundances, while their nitrogen to carbon abundance ratios appear to vary by at least as much and probably more than that found in the Galactic sample.

Effect of osteoporosis on bone mineral density and fracture repair in a rat femoral fracture model

Osteoporosis (OP) is one of the most prevalent bone diseases worldwide with bone fracture the major clinical consequence. The effect of OP on fracture repair is disputed and although it might be expected for fracture repair to be delayed in osteoporotic individuals, a definitive answer to this question still eludes us. The aim of this study was to clarify the effect of osteoporosis in a rodent fracture model. OP was induced in 3-month-old rats (n = 53) by ovariectomy (OVX) followed by an externally fixated, mid-diaphyseal femoral osteotomy at 6 months (OVX group). A further 40 animals underwent a fracture at 6 months (control group). Animals were sacrificed at 1, 2, 4, 6, and 8 weeks postfracture with outcome measures of histology, biomechanical strength testing, pQCT, relative BMD, and motion detection. OVX animals had significantly lower BMD, slower fracture repair (histologically), reduced stiffness in the fractured femora (8 weeks) and strength in the contralateral femora (6 and 8 weeks), increased body weight, and decreased motion. This study has demonstrated that OVX is associated with decrease in BMD (particularly in trabecular bone) and a reduction in the mechanical properties of intact bone and healing fractures. The histological, biomechanical, and radiological measures of union suggest that OVX delayed fracture healing. (C) 2007 Orthopaedic Research Society. Published by Wiley Periodicals.

Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.