Optimizing Phylogenetic Supertrees Using Answer Set Programming

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.Comment: To appear in Theory and Practice of Logic Programming (TPLP), Proceedings of ICLP 201

Optical properties of nanoclusters from time-dependent density-functional theory

The ground state properties of a quantum-mechanical many-electron system can be effectively modeled by its total electron density only, which is the key idea of the density-functional theory (DFT) methods. However, electronic excitations to higher energy states are not adequately described by the standard DFT formalism. To model the optical properties, for example, absorption and emission and response to time-dependent fields such as laser fields, the extension to time-dependent DFT (TDDFT) has become a popular method. In this Thesis, the TDDFT methods are utilized to calculate the optical properties of various nanostructures including fullerenes and fullerene derivatives, silicon nanocrystals and metal-polymer hybrid structures. The main focus is in the determination of their photoabsorption spectra using a real-space implementation of TDDFT. By these calculations we study how different structural variations and changes in the chemical environment affect the electronic and optical properties of the materials. For carbon and boron nitride fullerenes, variations in their size, geometry and doping are found to have a clear impact on their photoabsorption spectra. The results strengthen the view that optical absorption can be effectively used in the experimental characterization of such structures, for example in distinguishing between different isomers. The photoabsorption is observed to be strongly affected by the chemical environment for both silicon nanocrystals and small silver nanoclusters. When silicon nanoclusters are embedded in silica, the size dependence of their absorption edge is found to change due to major changes in the electronic structure. For the silver clusters, the presence of a polymer is found to bring the absorption edge down to the visible range in some of the studied cases. These calculations shed light to the experimental observations of unexpected absorption from such structures in the visible range

Tunability of the optical absorption in small silver cluster-polymer hybrid systems

We have calculated the absorption characteristics of different hybrid systems consisting of Ag, Ag2 or Ag3 atomic clusters and poly(methacrylic acid) (PMAA) 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, the leading absorption edge can be shifted up to about 4.5 eV. The results give theoretical support to the experimental observations on the absorption in the visible range in metal cluster-polymer hybrid structures.Comment: Updated layout and minor changes in versions 2 and

Photoabsorption spectra of small fullerenes and Si-heterofullerenes

We study the spectral properties of two kinds of derivatives of the carbon fullerene C60, 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. C20, C28, C32, C36, and C50, the most stable small fullerenes in the range of C20–C50, are found to have characteristic features in their optical absorptionspectra, 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 dopedfullerenes 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 dopingC60 up to C48Si12 so that absorption in the visible and near infrared regions increases.Peer reviewe

Photoabsorption spectra of boron nitride fullerenelike structures

Optical absorption spectra have been calculated for a series of boron nitride fullerenelike cage structures BnNn 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.Peer reviewe

Effect of the surrounding oxide on the photoabsorption spectra of Si nanocrystals

A systematic study of the optical absorption of small silicon nanocrystals (Si-NCs) 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 SiO2. 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.Peer reviewe

Temporal patterns of phytoplankton phenology across high latitude lakes unveiled by long-term time series of satellite data

Monitoring temporal changes in phytoplankton dynamics in high latitude lakes is particularly timely for understanding the impacts of warming on aquatic ecosystems. In this study, we analyzed 33-years of high resolution (30 m) Landsat (LT) data for reconstructing seasonal patterns of chlorophyll a (chl a) concentration in four lakes across Finland, between 60°N and 64°N. Chl a models based on LT spectral bands were calibrated using 17-years (2000–2016) of field measurements collected across the four lakes. These models were then applied for estimating chl a using the entire LT-5 and 7 archives. Approximately 630 images, from 1984 to 2017, were analyzed for each lake. The chl a seasonal patterns were characterized using phenology metrics, and the time-series of LT-based chl a estimates were used for identifying temporal shifts in the seasonal patterns of chl a concentration. Our results showed an increase in the length of phytoplankton growth season in three of the lakes. The highest increase was observed in Lake Köyliönjärvi, where the length of growth season has increased by 28 days from the baseline period of 1984–1994 to 2007–2017. The increase in the length of season was mainly attributed to an earlier start of phytoplankton blooms. We further analyzed surface temperature (Ts) and precipitation data to verify if climatic factors could explain the shifts in the seasonal patterns of chl a. We found no direct relationship between Ts and chl a seasonal patterns. Similarly, the phenological metrics of Ts, in particular length of season, did not show significant temporal trends. On the other hand, we identify potential links between changes in precipitation patterns and the increase in the phytoplankton season length. We verified a significant increase in the rainfall contribution to the total precipitation during the autumn and winter, accompanied by a decline in snowfall volumes. This could indicate an increasing runoff volume during the beginning of spring, contributing to an earlier onset of the phytoplankton blooms, although further assessments are needed to analyze historical streamflow values and nearby land cover data. Likewise, additional studies are needed to better understand why chl a patterns in some lakes seem to be more resilient than in others.peerReviewe

Hoiva-avustajaselvitys. Joustava koulutus- ja työllistymisväylä sosiaali- ja terveyspalveluiden avustaviin tehtäviin

Joustava kouluttautumis- ja työllistymisväylä sosiaali- ja terveysalan avustaviin tehtäviin on yksi keino varmistaa alan henkilöstön riittävyyttä. Hoiva-avustajan valmistava koulutus muodostuu lähihoitajatutkinnon kahdesta tutkinnon osasta ja yhdestä valinnaisesta osasta, joka tukee koulutettavan työskentelyä joko vanhus- tai vammaispalveluissa. Tämä selvitys pyrkii vastaamaan kysymyksiin siitä, miten ja mihin hoiva-avustajakoulutuksen suorittaneet ovat työllistyneet, miten koulutus vastaa työelämän tarpeisiin, minkälaisia kokemuksia koulutuksesta on työnantajilla ja koulutetuilla sekä minkälaisia tehtäviä hoiva-avustajat tekevät. Selvitys perustuu TEM:n rekisteritietoihin, koulutetuille tehtyyn kyselyyn sekä työnantajien haastatteluihin. Selvitys osoitti, että pääsääntöisesti koulutukseen oltiin tyytyväisiä, mutta hoitoon ja huolenpitoon liittyvää osuutta toivottiin lisää. Koulutuksen jälkeen noin puolet valmistuneista työllistyi. Työssä olleet hoiva-avustajat olivat tyytyväisiä työhönsä, joka useimmiten löytyi vanhus- ja vammaispalveluista. Osa työnantajista palkkasi mielellään hoiva-avustajia, osa oli epäröiviä. Lähihoitajan ja hoiva-avustajan tehtävien jakoa tulee edelleen kehittää, ja lääkehoidon osalta on selkiytettävä, mikä on sallittua, mikä ei. Tiedotusta koulutuksesta ja hoiva-avustajien tehtävän kuvasta on lisättävä. Pienen aineiston vuoksi olisi kerättävä lisää tietoa hoiva-avustajien saamisesta ja työstä vanhuspalvelulain toimeenpanon yhteydessä