Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

Numerical simulations of unsteady wet steam flows with non-equilibrium condensation in the nozzle and the steam turbine

Numerical techniques for non-equilibrium condensing flows are presented. Conservation equations for homogeneous gas-liquid two-phase compressible flows are solved by using a finite volume method based on an approximate Riemann solver. The phase change consists of the homogeneous nucleation and growth of existing droplets. Nucleation is computed with the classical Volmer-Frenkel model, corrected for the influence of the droplet temperature being higher than the steam temperature due to latent heat release. For droplet growth, two types of heat transfer model between droplets and the surrounding steam are used: a free molecular flow model and a semi-empirical two-layer model which is deemed to be valid over a wide range of Knudsen number. The computed pressure distribution and Sauter mean droplet diameters in a convergent-divergent (Laval) nozzle are compared with experimental data. Both droplet growth models capture qualitatively the pressure increases due to sudden heat release by the non-equilibrium condensation. However the agreement between computed and experimental pressure distributions is better for the two-layer model. The droplet diameter calculated by this model also agrees well with the experimental value, whereas that predicted by the free molecular model is too small. Condensing flows in a steam turbine cascade are calculated at different Mach numbers and inlet superheat conditions and are compared with experiments. Static pressure traverses downstream from the blade and pressure distributions on the blade surface agree well with experimental results in all cases. Once again, droplet diameters computed with the two-layer model give best agreement with the experiments. Droplet sizes are found to vary across the blade pitch due to the significant variation in expansion rate. Flow patterns including oblique shock waves and condensation-induced pressure increases are also presented and are similar to those shown in the experimental Schlieren photographs. Finally, calculations are presented for periodically unsteady condensing flows in a low expansion rate, convergent-divergent (Laval) nozzle. Depending on the inlet stagnation subcooling, two types of self-excited oscillations appear: a symmetric mode at lower inlet subcooling and an asymmetric mode at higher subcooling. Plots of oscillation frequency versus inlet sub-cooling exhibit a hysteresis loop, in accord with observations made by other researchers for moist air flow. Copyright © 2006 by ASME.

Collapse of a composite beam made from ultra high molecular-weight polyethylene fibres

Hot-pressed laminates with a [0/90]48 lay-up, consisting of 83% by volume of ultra high molecular-weight polyethylene (UHMWPE) fibres, and 17% by volume of polyurethane (PU) matrix, were cut into cantilever beams and subjected to transverse end-loading. The collapse mechanisms were observed both visually and by X-ray scans. Short beams deform elastically and collapse plastically in longitudinal shear, with a shear strength comparable to that observed in double notch, interlaminar shear tests. In contrast, long cantilever beams deform in bending and collapse via a plastic hinge at the built-in end of the beam. The plastic hinge is formed by two wedge-shaped microbuckle zones that grow in size and in intensity with increasing hinge rotation. This new mode of microbuckling under macroscopic bending involves both elastic bending and shearing of the plies, and plastic shear of the interface between each ply. The double-wedge pattern contrasts with the more usual parallel-sided plastic microbuckle that occurs in uniaxial compression. Finite element simulations and analytical models give additional insight into the dominant material and geometric parameters that dictate the collapse response of the UHMWPE composite beam in bending. Detailed comparisons between the observed and predicted collapse responses are used in order to construct a constitutive model for laminated UHMWPE composites. © 2013 Elsevier Ltd.