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.

Tuning of the electronic characteristics of ZnO nanowire field effect transistors by proton irradiation.

We demonstrated a controllable tuning of the electronic characteristics of ZnO nanowire field effect transistors (FETs) using a high-energy proton beam. After a short proton irradiation time, the threshold voltage shifted to the negative gate bias direction with an increase in the electrical conductance, whereas the threshold voltage shifted to the positive gate bias direction with a decrease in the electrical conductance after a long proton irradiation time. The electrical characteristics of two different types of ZnO nanowires FET device structures in which the ZnO nanowires are placed on the substrate or suspended above the substrate and photoluminescence (PL) studies of the ZnO nanowires provide substantial evidence that the experimental observations result from the irradiation-induced charges in the bulk SiO(2) and at the SiO(2)/ZnO nanowire interface, which can be explained by a surface-band-bending model in terms of gate electric field modulation. Our study on the proton-irradiation-mediated functionalization can be potentially interesting not only for understanding the proton irradiation effects on nanoscale devices, but also for creating the property-tailored nanoscale devices.

UV photoconductivity characteristics of ZnO nanowire field effect transistor treated by proton irradiation

We investigated the UV photoconductivity characteristics of ZnO nanowire field effect transistors (FETs) irradiated by proton beams. After proton beam irradiation (using a beam energy of 10 MeV and a fluence of 10 12 cm -2), the drain current and carrier density in the ZnO nanowire FETs decreased, and the threshold voltage shifted to the positive gate bias direction due to the creation of interface traps at the SiO 2/ZnO nanowire interface by the proton beam. The interface traps produced a higher surface barrier potential and a larger depletion region at the ZnO nanowire surface, affecting the photoconductivity and its decay time. The UV photoconductivity of the proton-irradiated ZnO nanowire FETs was higher and more prolonged than that of the pristine ZnO nanowire FETs. The results extend our understanding of the UV photoconductivity characteristics of ZnO nanowire devices and other materials when irradiated with highly energetic particles. © 2012 Elsevier B.V. All rights reserved.