Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method.

Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, ΔSCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.

Biomechanical determinants of maximal stair climbing capacity in healthy elderly women.

Stair walking is an important functional movement task that may require considerable amounts of muscle strength/power. This study aimed to perform a descriptive biomechanical analysis of maximal stair ascent in elderly women and to examine the relationship between mechanical muscle function and maximal stair ascending velocity (MAV). Seventeen healthy elderly women (age 72.4 +/- 6.4) were tested for MAV, maximal multi-joint counter movement jumping (CMJ), and maximal single-joint isokinetic/isometric muscle moment. Peak knee joint power during MAV was the single independent parameter that explained most of the variation in MAV (50%), however, combining knee and ankle parameters in a multiple regression analysis mean joint power explained 82.4% of the variation in MAV. Generally, multi-joint CMJ parameters showed stronger correlations with MAV than single-joint isokinetic/isometric muscle strength parameters. MAV appeared to be highly dependent upon knee and ankle power and to a lesser extent on joint moment and range of motion. Furthermore, CMJ assessment seemed well applicable in healthy elderly individuals to distinguish between differentiated levels of maximal stair walking capacity.

Muscle performance following fatigue induced by isotonic and quasi-isometric contractions of rat extensor digitorum longus and soleus muscles in vitro.

AIM: To study the effect of contraction mode on fatigue development. METHODS: Muscle fatigue was induced by isotonic and quasi-isometric contractions in rat soleus (SOL) and extensor digitorum longus (EDL) muscles, using identical stimulation protocol (60 Hz, 400 ms s-1) for 100 s in SOL and 60 s in EDL. Fatigue was quantified as the decline in peak values of shortening, shortening velocity, relaxation and work during the isotonic contractions, and, correspondingly, of force, rate of force development, relaxation and work during the quasi-isometric contractions. Maximal test contractions (60 Hz, 1.5 s) performed before and after fatigue were analysed for decline in force development (Fmax), rate of force development (dF/dtmax) and relaxation (-dF/dtmax). RESULTS: Fmax declined to significantly lower values after isotonic than after quasi-isometric fatiguing contractions (fatigued in percentage of unfatigued): 58.5 +/- 6.4% vs. 64.4 +/- 7.0% in SOL, and 30.4 +/- 4.1% vs. 33.3 +/- 3.6% in EDL, respectively. The same pattern was seen for dF/dtmax which decreased to: 46.3 +/- 9.9% vs. 52.3 +/- 8.5% in SOL, and 19.1 +/- 4.3% vs. 22.3 +/- 3.2% in EDL after isotonic and quasi-isometric contractions, respectively. Similarly, when comparing fatigue development during the two contraction modes, the respective fatigue variables decreased more rapidly and to lower levels during isotonic vs. quasi-isometric contractions. During maximal test contractions, the dynamic fatigue variables (+/-dF/dtmax) declined to significantly lower levels than Fmax. CONCLUSIONS: Fatigue development was significantly larger during isotonic vs. quasi-isometric contractions. The use of force as the only experimental fatigue variable may underestimate the functional impairment of fatigued muscle, neglecting the fatigue effect on time and length dimensions.

Interactions between ecto- and endoparasites in trout Salmo trutta.

Trout fry were experimentally infected with endoparasites (Anisakis sp.) and/or ectoparasites (Gyrodactylus derjavini). During the following 3 weeks the infection level of G. derjavini was significantly lowered in fish infected with live anisakids compared to fish injected with physiological saline, a corresponding amount of Anisakis protein sonicate or to untreated fish. Subsequent scanning electron microscopy (SEM) of recovered nematodes from the trout showed an extensive colonization of the worms with host macrophages. It is indicated that the activation of the fish immune system by infection with live anisakids influences the skin response of the host with a subsequent negative effect on the ectoparasites G. derjavini.

Genetic tagging of humpback whales.

The ability to recognize individual animals has substantially increased our knowledge of the biology and behaviour of many taxa. However, not all species lend themselves to this approach, either because of insufficient phenotypic variation or because tag attachment is not feasible. The use of genetic markers ('tags') represents a viable alternative to traditional methods of individual recognition, as they are permanent and exist in all individuals. We tested the use of genetic markers as the primary means of identifying individuals in a study of humpback whales in the North Atlantic Ocean. Analysis of six microsatellite loci among 3,060 skin samples collected throughout this ocean allowed the unequivocal identification of individuals. Analysis of 692 'recaptures', identified by their genotype, revealed individual local and migratory movements of up to 10,000 km, limited exchange among summer feeding grounds, and mixing in winter breeding areas, and also allowed the first estimates of animal abundance based solely on genotypic data. Our study demonstrates that genetic tagging is not only feasible, but generates data (for example, on sex) that can be valuable when interpreting the results of tagging experiments.

Populations genetic analysis of nuclear and mitochondrial loci in skin biopsies collected from central and northeastern North Atlantic humpback whales (Megaptera novaeangliae): population identity and migratory destinations.

It has been speculated that humpback whales, Megaptera novaeangliae, from the northeastern North Atlantic breed in tropical waters off the coast of West Africa and therefore that they represent a separate breeding population from that which winters in the West Indies. We determined the genotype at six microsatellite loci as well as the sequence of the first 288 nucleotides in the mitochondrial control region of 133 skin biopsies collected from humpback whales in the central North Atlantic (Iceland and Jan Mayen) and the northeastern North Atlantic (Bear Island and the northern coast of Norway). We detected no significant deviations from Hardy-Weinberg proportions nor any differences in genotype frequencies between localities at the nuclear loci. However, the mitochondrial analyses revealed two distinct matrilineal aggregations: the central and the northeastern North Atlantic. Our findings were not compatible with the idea of a separate eastern North Atlantic breeding ground unless one has been established recently. The proposed alternative hypothesis of a common North Atlantic panmictic population (wintering primarily in the West Indies) in which individual whales display maternally directed site-fidelity to specific feeding grounds was supported by re-sightings of two northeastern North Atlantic humpback whales in the West Indies.