Computational Physics on Graphics Processing Units

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

Photosystem-II D1 protein mutants of Chlamydomonas reinhardtii in relation to metabolic rewiring and remodelling of H-bond network at Q(B) site

Photosystem II (PSII) reaction centre D1 protein of oxygenic phototrophs is pivotal for sustaining photosynthesis. Also, it is targeted by herbicides and herbicide-resistant weeds harbour single amino acid substitutions in D1. Conservation of D1 primary structure is seminal in the photosynthetic performance in many diverse species. In this study, we analysed built-in and environmentally-induced (high temperature and high photon fluency-HT/HL) phenotypes of two D1 mutants of Chlamydomonas reinhardtii with Ala250Arg (A250R) and Ser264Lys (S264K) substitutions. Both mutations differentially affected efficiency of electron transport and oxygen production. In addition, targeted metabolomics revealed that the mutants undergo specific differences in primary and secondary metabolism, namely, amino acids, organic acids, pigments, NAD, xanthophylls and carotenes. Levels of lutein, beta-carotene and zeaxanthin were in sync with their corresponding gene transcripts in response to HT/HL stress treatment in the parental (IL) and A250R strains. D1 structure analysis indicated that, among other effects, remodelling of H-bond network at the Q(B) site might underpin the observed phenotypes. Thus, the D1 protein, in addition to being pivotal for efficient photosynthesis, may have a moonlighting role in rewiring of specific metabolic pathways, possibly involving retrograde signalling

A global analysis of the comparability of winter chill models for fruit and nut trees

Many fruit and nut trees must fulfill a chilling requirement to break their winter dormancy and resume normal growth in spring. Several models exist for quantifying winter chill, and growers and researchers often tacitly assume that the choice of model is not important and estimates of species chilling requirements are valid across growing regions. To test this assumption, Safe Winter Chill (the amount of winter chill that is exceeded in 90% of years) was calculated for 5,078 weather stations around the world, using the Dynamic Model [in Chill Portions (CP)], the Chilling Hours (CH) Model and the Utah Model [Utah Chill Units (UCU)]. Distributions of the ratios between different winter chill metrics were mapped on a global scale. These ratios should be constant if the models were strictly proportional. Ratios between winter chill metrics varied substantially, with the CH/CP ratio ranging between 0 and 34, the UCU/CP ratio between −155 and +20 and the UCU/CH ratio between −10 and +5. The models are thus not proportional, and chilling requirements determined in a given location may not be valid elsewhere. The Utah Model produced negative winter chill totals in many Subtropical regions, where it does not seem to be useful. Mean annual temperature and daily temperature range influenced all winter chill ratios, but explained only between 12 and 27% of the variation. Data on chilling requirements should always be amended with information on the location and experimental conditions of the study in which they were determined, ideally including site-specific conversion factors between winter chill models. This would greatly facilitate the transfer of such information across growing regions, and help prepare growers for the impact of climate change

Factors associated with diversity, quantity and zoonotic potential of ectoparasites on urban mice and voles

Wild rodents are important hosts for tick larvae but co-infestations with other mites and insects are largely neglected. Small rodents were trapped at four study sites in Berlin, Germany, to quantify their ectoparasite diversity. Host-specific, spatial and temporal occurrence of ectoparasites was determined to assess their influence on direct and indirect zoonotic risk due to mice and voles in an urban agglomeration. Rodent-associated arthropods were diverse, including 63 species observed on six host species with an overall prevalence of 99%. The tick Ixodes ricinus was the most prevalent species, found on 56% of the rodents. The trapping location clearly affected the presence of different rodent species and, therefore, the occurrence of particular host-specific parasites. In Berlin, fewer temporary and periodic parasite species as well as non-parasitic species (fleas, chiggers and nidicolous Gamasina) were detected than reported from rural areas. In addition, abundance of parasites with low host-specificity (ticks, fleas and chiggers) apparently decreased with increasing landscape fragmentation associated with a gradient of urbanisation. In contrast, stationary ectoparasites, closely adapted to the rodent host, such as the fur mites Myobiidae and Listrophoridae, were most abundant at the two urban sites. A direct zoonotic risk of infection for people may only be posed by Nosopsyllus fasciatus fleas, which were prevalent even in the city centre. More importantly, peridomestic rodents clearly supported the life cycle of ticks in the city as hosts for their subadult stages. In addition to trapping location, season, host species, body condition and host sex, infestation with fleas, gamasid Laelapidae mites and prostigmatic Myobiidae mites were associated with significantly altered abundance of I. ricinus larvae on mice and voles. Whether this is caused by predation, grooming behaviour or interaction with the host immune system is unclear. The present study constitutes a basis to identify interactions and vector function of rodent-associated arthropods and their potential impact on zoonotic diseases

Development of a photosynthesis model with an emphasis on ecological applications

A theoretical description of the simultaneous processes of photosynthesis and photorespiration in a single leaf is developed, based on the hypothesis that carbon dioxide and oxygen compete for the active site of ribulose diphosphate carboxylase. Michaelis-Menten kinetics and competitive inhibition at the end of a diffusion path provide the basic structure of the model. Data of Ludwig (1972) from sunflower are analyzed according to the formulation. This description is part of a more general physiological-ecological model of photosynthesis presented previously (Tenhunen et al., 1976a, b) and continues to elaborate sub-processes in terms of physiologically meaningful parameters. The description is considered a working hypothesis. Data on photorespiration from the literature are reviewed as they relate to this working hypothesis. Several lines of investigation are thereby suggested that will help clarify the role of photorespiration in whole leaf photosynthesis and determine the over-all utility of this modeling approach.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47718/1/442_2005_Article_BF01833627.pd

A model describing photosynthesis in terms of gas diffusion and enzyme kinetics

A model predicting net photosynthesis of individual plant leaves for a variety of environmental conditions has been developed. It is based on an electrical analogue describing gas diffusion from the free atmosphere to the sites of CO 2 fixation and a Michaelis-Menten equation describing CO 2 fixation. The model is presented in two versions, a simplified form without respiration and a more complex form including respiration. Both versions include terms for light and temperature dependence of CO 2 fixation and light control of stomatal resistance. The second version also includes terms for temperature, light, and oxygen dependence of respiration and O 2 dependence of CO 2 fixation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47495/1/425_2004_Article_BF00387066.pd

Biological control of ticks

Ticks have numerous natural enemies, but only a few species have been evaluated as tick biocontrol agents (BCAs). Some laboratory results suggest that several bacteria are pathogenic to ticks, but their mode of action and their potential value as biocontrol agents remain to be determined. The most promising entomopathogenic fungi appear to be Metarhizium anisopliae and Beauveria bassiana, strains of which are already commercially available for the control of some pests. Development of effective formulations is critical for tick management. Entomopathogenic nematodes that are pathogenic to ticks can potentially control ticks, but improved formulations and selection of novel nematode strains are needed. Parasitoid wasps of the genus Ixodiphagus do not typically control ticks under natural conditions, but inundative releases show potential value. Most predators of ticks are generalists, with a limited potential for tick management (one possible exception is oxpeckers in Africa). Biological control is likely to play a substantial role in future IPM programmes for ticks because of the diversity of taxa that show high potential as tick BCAs. Considerable research is required to select appropriate strains, develop them as BCAs, establish their effectiveness, and devise production strategies to bring them to practical use. © 2004 Cambridge University Press

Anti-tick biological control agents: Assessment and future perspectives

INTRODUCTION Since the beginning of the twentieth century investigators have documented numerous potential tick biological control agents, including pathogens, parasitoids and predators of ticks (Jenkins, 1964; Mwangi, 1991; Mwangi et al., 1991; Samish & Rehacek, 1999; Kaaya, 2003; Ostfeld et al., 2006). Several authors have reviewed specific groups of natural enemies of ticks, including pathogens (Lipa, 1971; Hoogstraal, 1977; Chandler et al., 2000), nematodes (Samish, Alekseev & Glazer, 2000a, 2000b; Samish & Glazer, 2001), parasitoids (Cole, 1965; Trjapitzin, 1985; Davis, 1986; Mwangi & Kaaya, 1997; Hu, Hyland & Oliver, 1998; Knipling & Steelman, 2000) and predators (Barre et al., 1991; Mwangi, Newson & Kaaya, 1991; Kok & Petney, 1993; Samish & Alexseev, 2001). In practice, ticks are controlled at present mostly by chemical acaricides (see Chapter 18). However, biological control is becoming an increasingly attractive approach to tick management because of: (1) increasing concerns about environmental safety and human health (e.g. the gradual increase in use of chemical insecticides in several countries is stimulating the growing market of \u27organic\u27 food); (2) the increasing costs of chemical control; and (3) the increasing resistance of ticks to pesticides. To date, biocontrol has been targeted largely at pests of plants, with only a few efforts to introduce biocontrol agents for the control of ticks. Nevertheless, the knowledge and experience accumulated in plant protection will aid in the development of tick biocontrol methods