A systematic study of the optical absorption of small silicon nanocrystals ͑Si-NCs͒ embedded in silicon dioxide is performed using real-time time-dependent density-functional theory. The modeled Si-NCs contain up to 47 Si atoms with the surrounding oxide being described by a shell of SiO 2 . The oxide-embedded Si-NCs exhibit absorption spectra that differ significantly from the spectra of the hydrogen-passivated Si-NCs. In particular, the minimum absorption energy is found to decrease when the Si-NCs are exposed to dioxide coating. Unexpectedly, the absorption energy of the oxide-embedded Si-NCs remains approximately constant for core sizes down to 17 atoms, whereas the absorption energy of the hydrogen-passivated Si-NCs increases with decreasing crystal size. This trend suggests a different mechanism for producing the lowest-energy excitations in these two cases.

We have calculated the absorption characteristics of different hybrid systems consisting of Ag, Ag 2 , or Ag 3 atomic clusters and poly͑methacrylic acid͒ using the time-dependent density-functional theory. The polymer is found to have an extensive structural-dependency on the spectral patterns of the hybrid systems relative to the bare clusters. The absorption spectrum can be "tuned" to the visible range for hybrid systems with an odd number of electrons per silver cluster, whereas for hybrid systems comprising an even number of electrons per silver cluster, the leading absorption edge can be shifted up to ϳ4.5 eV. The results give theoretical support to the experimental observations on the absorption in the visible range in metal cluster-polymer hybrid structures.

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are as consistent with the source trees as possible. This leads to an optimization problem that is computationally challenging and typically heuristic methods, such as matrix representation with parsimony (MRP), are used. In this paper we consider the use of answer set programming to solve the supertree construction problem in terms of two alternative encodings. The first is based on an existing encoding of trees using substructures known as quartets, while the other novel encoding captures the relationships present in trees through direct projections. We use these encodings to compute a genus-level supertree for the family of cats (Felidae). Furthermore, we compare our results to recent supertrees obtained by the MRP method.

Optical absorption spectra have been calculated for a series of boron nitride fullerenelike cage structures B n N n of sizes n = 12-36. The method used is a real-time, real-space implementation of the time-dependent density-functional theory, involving the full time propagation of the time-dependent Kohn-Sham equations. The spectra are found to be a possible tool for distinguishing between different boron nitride fullerene species and isomers. The trends and differences in the spectra are found to be related to the general geometry of the molecules. Comparison between local-density and generalized-gradient approximations for electron exchange-correlation functionals shows that both of them produce essentially the same spectral characteristics.

We study the spectral properties of two kinds of derivatives of the carbon fullerene C 60 , small fullerenes and Si-heterofullerenes, by ab initio calculations. The principal method of study is the time-dependent density-functional theory in its full time-propagation form. C 20 , C 28 , C 32 , C 36 , and C 50 , the most stable small fullerenes in the range of C 20 -C 50 , are found to have characteristic features in their optical absorption spectra, originating from the geometry of the molecules in question. The comparison of measured and calculated absorption spectra is found to be a useful tool in differentiating between different, almost isoenergetic ground state structure candidates of small fullerenes. Substitutionally doped fullerenes are of interest due to their enhanced chemical reactivity. It is suggested that the doping degree can be obtained by studying the absorption spectra. For example, it is observed that the spectra gradually change when doping C 60 up to C 48 Si 12 so that absorption in the visible and near infrared regions increases.