Asymptotic Analysis of the Current-Voltage Curve of a pnpn Semiconductor Device

We consider the one-dimensional steady-state semiconductor deviceequations modelling a pnpn device. There are two relevant scalingsof the equations corresponding to small and large applied voltages.In both scalings, the semiconductor equations can be consideredas singularly perturbed. It turns out that the small-voltagescaling breaks down for current values between two saturationcurrents. In that interval, the large-voltage scaling has tobe employed. For both scalings, we derive the first-order termsof an asymptotic expansion and show that the reduced problemhas a solution. An example verifies that the current-voltagecurves obtained have the expected qualitative structure.     

Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.     

Stage effects of negative emotion on spatial and verbal working memory

Background  

The effects of negative emotion on different processing periods in spatial and verbal working memory (WM) and the possible brain mechanism of the interaction between negative emotion and WM were explored using a high-time resolution event-related potential (ERP) technique and time-locked delayed matching-to-sample task (DMST).     

A Computational Study of Vicinal Fluorination in 2,3‐Difluorobutane: Implications for Conformational Control in Alkane Chains

A comprehensive conformational analysis of both 2,3‐difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2‐difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3‐difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn‐difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control.     

Achieving plane wave accuracy in linear-scaling density functional theory applied to periodic systems: a case study on crystalline silicon

Linear-scaling methods for density functional theory promise to revolutionize the scope and scale of first-principles quantum mechanical calculations. Crystalline silicon has been the system of choice for exploratory tests of such methods in the literature, yet attempts at quantitative comparisons under linear-scaling conditions with traditional methods or experimental results have not been forthcoming. A detailed study using the ONETEP code is reported here, demonstrating for the first time that plane wave accuracy can be achieved in linear-scaling calculations on periodic systems.     

Pulay forces from localized orbitals optimized in situ using a psinc basis set

In situ optimization of a set of localized orbitals with respect to a systematically improvable basis set independent of the position of the atoms, such as psinc functions, would theoretically eliminate the correction due to Pulay forces from the total ionic forces. We demonstrate that for strict localization constraints, especially with small localization regions, there can be non-negligible Pulay forces that must be calculated as a correction to the Hellmann-Feynman forces in the ground state. Geometry optimization calculations, which rely heavily upon accurate evaluation of the total ionic forces, show much better convergence when Pulay forces are included. The more conventional case, where the local orbitals remain fixed to pseudo-atomic orbital multiple-ζ basis sets, also benefits from this implementation. We have validated the method on several test cases, including a DNA fragment with 1045 atoms.     

Torsional anharmonicity in the conformational analysis of beta-D-galactose

Schemes to include a treatment of torsional anharmonicity in the conformational analysis of biological molecules are introduced. The approaches combine ab initio electronic energies and harmonic frequencies with anharmonic torsional partition functions calculated using the torsional path integral Monte Carlo method on affordable potential energy surfaces. The schemes are applied to the conformational study of the monosaccharide beta-d-galactose in the gas phase. The global minimum structure is almost exclusively populated at 100 K, but a large number of conformers are present at ambient and higher temperatures. Both quantum mechanical and anharmonic effects in the torsional modes have little effect on the populations at all temperatures considered, and it is, therefore, expected that standard harmonic treatments are satisfactory for the conformational study of monosaccharides.     

Introducing ONETEP: linear-scaling density functional simulations on parallel computers

We present ONETEP (order-N electronic total energy package), a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and the number of processors. ONETEP is based on our reformulation of the plane wave pseudopotential method which exploits the electronic localization that is inherent in systems with a nonvanishing band gap. We summarize the theoretical developments that enable the direct optimization of strictly localized quantities expressed in terms of a delocalized plane wave basis. These same localized quantities lead us to a physical way of dividing the computational effort among many processors to allow calculations to be performed efficiently on parallel supercomputers. We show with examples that ONETEP achieves excellent speedups with increasing numbers of processors and confirm that the time taken by ONETEP as a function of increasing number of atoms for a given number of processors is indeed linear. What distinguishes our approach is that the localization is achieved in a controlled and mathematically consistent manner so that ONETEP obtains the same accuracy as conventional cubic-scaling plane wave approaches and offers fast and stable convergence. We expect that calculations with ONETEP have the potential to provide quantitative theoretical predictions for problems involving thousands of atoms such as those often encountered in nanoscience and biophysics.     

Rare earth element (REE) in surface mangrove sediment by instrumental neutron activation analysis

A study is carried out on the concentrations of rare earth element (REE) elements present in surface mangrove sediments from 10 locations throughout west coast Malaysia. In carrying out the analysis, the best and most convenient method being the instrumental neutron activation analysis (INAA). Samples were obtained, dried, crushed to powdery form and samples prepared for INAA. All the samples for analysis were weighted approximately 150 mg for short irradiation and 200 mg for long irradiation time. As calibration and quality control procedures, blank samples, standard reference material SL-1 were then irradiated with thermal neutron flux of 4 × 10¹² cm^?2 s^?1 at the MINT TRIGA Mark II research reactor which operated at 750 kW by using a pneumatic transport facility. The REE elements of surface sediment samples in this study are Dy, Sm, Eu,Yb, Lu, Tb, La and Ce. It was found that the level of concentrations of all the REE elements varies in the range (0.35–117.4 mg/kg). The geochemical behavior of REEs in surface sediments and normalized pattern (chondrite and shale) has been studied. The degree of sediments contaminations were computed using an enrichment factor. The results showed that the enrichment factor varied in the range (0.75–6.75).