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.

QM/MM simulation of liquid water with an adaptive quantum region.

The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.

Design and market considerations for axial flux superconducting electric machine design

In this paper, the authors investigate a number of design and market considerations for an axial flux superconducting electric machine design that uses high temperature superconductors. The axial flux machine design is assumed to utilise high temperature superconductors in both wire (stator winding) and bulk (rotor field) forms, to operate over a temperature range of 65-77 K, and to have a power output in the range from 10s of kW up to 1 MW (typical for axial flux machines), with approximately 2-3 T as the peak trapped field in the bulk superconductors. The authors firstly investigate the applicability of this type of machine as a generator in small- and medium-sized wind turbines, including the current and forecasted market and pricing for conventional turbines. Next, a study is also carried out on the machine's applicability as an in-wheel hub motor for electric vehicles. Some recommendations for future applications are made based on the outcome of these two studies. Finally, the cost of YBCO-based superconducting (2G HTS) wire is analysed with respect to competing wire technologies and compared with current conventional material costs and current wire costs for both 1G and 2G HTS are still too great to be economically feasible for such superconducting devices.