Practical Boundary Conditions for Electronic Structure Calculations

Computational materials design is an active area of research which aims at predicting physical and chemical properties of various materials from first-principles electronic structure calculations. To keep the computational costs manageable, the Schr¨odinger equations are often approximated by Kohn-Sham equations within the framework of density-functional theory. These Kohn-Sham equations are solved numerically either by a basis set expansion or real-space discretization under given boundary conditions. In the case of a plane-wave basis set, it is common practice to apply periodic boundary conditions in all directions, while isolated boundary conditions are more common for the atomic basis set. However, there are many other options besides these standard boundary conditions. In this presentation, we will explore several non-standard boundary conditions which exploit the characteristics of each system, such as surfaces, interfaces, and cyclic/helical structures, to minimize the computational costs of electronic structure calculations. Most of these boundary conditions are easily implemented by minor modifications of existing electronic structure codes. Numerical examples on a few model systems are also presented for the validation of these boundary conditions

Ab initio mass tensor molecular dynamics

Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy.Comment: 19 pages, 5 figure

Real Space Approach to Electronic-Structure Calculations

We have applied the Finite Element Method to the self-consistent electronic structure calculations of molecules and solids for the first time. In this approach all the calculations are performed in "real space" and the use of non-uniform mesh is made possible, thus enabling us to deal with localized systems with ease. To illustrate the utility of this method, we perform an all-electron calculation of hydrogen molecule in a supercell with LDA approximation. Our method is also applicable to mesoscopic systems.Comment: 11 pages, LaTeX, 5 figures available on request from [email protected]

Outbreak of Salmonella Braenderup Infection Originating in Boxed Lunches in Japan in 2008

There have been only 2 reports of a large-scale foodborne outbreak arising from Salmonella enterica serotype Braenderup infection worldwide. On August 9, 2008, an outbreak originating in boxed lunches occurred in Okayama, Japan. We conducted a cohort study of 786 people who received boxed lunches from a particular catering company and collected 644 questionnaires (response rate:82%). Cases were defined as those presenting with diarrhea (≧4 times in 24h) or fever (≧38℃) between 12 am on August 8 and 12 am on August 14. We identified 176 cases (women/men:39/137);younger children (aged＜10 years) appeared to more frequently suffer severe symptoms. Three food items were significantly associated with higher risk of illness;tamagotoji (soft egg with mixed vegetables and meat) (relative risk (RR):11.74, 95% confidence interval (CI):2.98-46.24), pork cooked in soy sauce (RR:3.17, 95% CI:1.24-8.10), and vinegared food (RR:4.13, 95% CI:1.60-10.63). Among them, only the RR of tamagotoji was higher when we employed a stricter case definition. Salmonella Braenderup was isolated from 5 of 9 sampled cases and 6 food handlers. It is likely that unpasteurized liquid eggs contaminated by Salmonella Braenderup and used in tamagotoji caused this outbreak