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- Hjorth Larsen, Ask, et al.
(författare)
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The atomic simulation environment-a Python library for working with atoms
- 2017
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Ingår i: Journal of Physics. - : Institute of Physics Publishing (IOPP). - 0953-8984 .- 1361-648X. ; 29:27
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Forskningsöversikt (refereegranskat)abstract
- The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.
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| 2. |
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| 3. |
- Antonsson, Jakob, et al.
(författare)
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Modeling Colloidal Particle Aggregation Using Cluster Aggregation with Multiple Particle Interactions
- 2024
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 128:18, s. 4513-4524
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigate the aggregation dynamics of colloidal silica by generating simulated structures and comparing them to experimental data gathered through scanning transmission electron microscopy (STEM). More specifically, diffusion-limited cluster aggregation and reaction-limited cluster aggregation models with different functions for the probability of particles sticking upon contact were used. Aside from using a constant sticking probability, the sticking probability was allowed to depend on the masses of the colliding clusters and on the number of particles close to the collision between clusters. The different models of the sticking probability were evaluated based on the goodness-of-fit of spatial summary statistics. Furthermore, the models were compared to the experimental data by calculating the structures’ fractal dimension and mass transport properties from simulations of flow and diffusion. The sticking probability, depending on the interaction with multiple particles close to the collision site, led to structures most similar to the STEM data.
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| 4. |
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| 5. |
- Augustin, Jakob, 1976, et al.
(författare)
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No evidence of genetic benefits from extra-pair fertilisations in female sand martins (Riparia riparia)
- 2007
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Ingår i: Journal of Ornithology. - : Springer Science and Business Media LLC. - 2193-7192 .- 2193-7206. ; 148:2, s. 189-198
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Tidskriftsartikel (refereegranskat)abstract
- Genetic parentage studies of socially monogamous birds reveal a widespread prevalence of extra-pair paternity. Variation in extra-pair paternity among individuals may depend on how different individuals benefit from extra-pair fertilisations and on the opportunity to pursue extra-pair copulations. A long-term study of sand martins (Riparia riparia) in Hungary allowed us to examine patterns of extra-pair fertilisations in a large colony of over 3,000 breeding pairs with many known age individuals. We used multi-locus DNA fingerprinting to determine whether extra-pair fertilisations occur when females are paired to (1) presumably low quality mates, or (2) genetically similar or dissimilar mates, and whether extra-pair fertilisations result in offspring of higher quality. Extra-paternal young were found in 38% of 47 broods and comprised 19% of 190 offspring. Males that lost paternity did not differ significantly from others in age or body condition. Social mates of broods containing extra-pair offspring did not differ in genetic similarity from pairs without extra-pair offspring. Furthermore, there was no significant difference in body condition between extra-pair young and their maternal half-siblings. We were unable to assign paternity and therefore cannot exclude the possibility that extra-pair males differed from the within-pair males they cuckolded, in age, body condition or genetic similarity with the female. We found a positive relationship between paternity losses and breeding density, suggesting that low breeding density may constrain opportunities for seeking extra-pair copulations.
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| 8. |
- Blomqvist, Jakob, et al.
(författare)
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Structure and Thermodynamical Properties of Zirconium Hydrides from First-Principle
- 2012
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Ingår i: Proceedings of the 15th international conference on environmental degradation of materials in nuclear power systems-water reactors. - Hoboken, New Jersey, Canada : John Wiley & Sons. - 9781118132418 - 9781118456835 ; , s. 671-679
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Zirconium alloys are used as nuclear fuel cladding material due to their mechanical and corrosion resistant properties together with their favorable cross-section for neutron scattering. At running conditions, however, there will be an increase of hydrogen in the vicinity of the cladding surface at the water side of the fuel.The hydrogen will diffuse into the cladding material and at certain conditions, such as lower temperatures and external load, hydrides will precipitate out in the material and cause well known embrittlement, blistering and other unwanted effects. Using phase-field methods it is now possible to model precipitation build-up in metals, for example as a function of hydrogen concentration, temperature and external load, but the technique relies on input of parameters, such as the formation energy of the hydrides and matrix. To that end, we have computed, using the density functional theory (DFT) code GPAW, the latent heat of fusion as well as solved the crystal structure for three zirconium hydride polymorphs: delta-ZrH1.6, gamma-ZrH, and epsilon-ZrH2.
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| 9. |
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| 10. |
- Chapman, Ben, et al.
(författare)
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To boldly go: individual differences in boldness influence migratory tendency.
- 2011
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X. ; 14, s. 871-876
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Tidskriftsartikel (refereegranskat)abstract
- Ecology Letters (2011) ABSTRACT: Partial migration, whereby only a fraction of the population migrates, is thought to be the most common type of migration in the animal kingdom, and can have important ecological and evolutionary consequences. Despite this, the factors that influence which individuals migrate and which remain resident are poorly understood. Recent work has shown that consistent individual differences in personality traits in animals can be ecologically important, but field studies integrating personality traits with migratory behaviour are extremely rare. In this study, we investigate the influence of individual boldness, an important personality trait, upon the migratory propensity of roach, a freshwater fish, over two consecutive migration seasons. We assay and individually tag 460 roach and show that boldness influences migratory propensity, with bold individuals being more likely to migrate than shy fish. Our data suggest that an extremely widespread personality trait in animals can have significant ecological consequences via influencing individual-level migratory behaviour.
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