| 1. |
- Crutchfield, J. P., et al.
(author)
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Objects that make objects: the population dynamics of structural complexity
- 2006
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:7, s. 345-349
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Journal article (peer-reviewed)abstract
- To analyse the evolutionary emergence of structural complexity in physical processes, we introduce a general, but tractable, model of objects that interact to produce new objects. Since the objects-epsilon-machines-have well-defined structural properties, we demonstrate that complexity in the resulting population dynamical system emerges on several distinct organizational scales during evolution-from individuals to nested levels of mutually self-sustaining interaction. The evolution to increased organization is dominated by the spontaneous creation of structural hierarchies and this, in turn, is facilitated by the innovation and maintenance of relatively low-complexity, but general individuals.
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| 2. |
- Gasser, T. Christian, et al.
(author)
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Hyperelastic modelling of arterial layers with distributed collagen fibre orientations
- 2006
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:6, s. 15-35
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Research review (peer-reviewed)abstract
- Constitutive relations are fundamental to the solution of problems in continuum mechanics, and are required in the study of, for example, mechanically dominated clinical interventions involving soft biological tissues. Structural continuum constitutive models of arterial layers integrate information about the tissue morphology and therefore allow investigation of the interrelation between structure and function in response to mechanical loading. Collagen fibres are key ingredients in the structure of arteries. In the media (the middle layer of the artery wall) they are arranged in two helically distributed families with a small pitch and very little dispersion in their orientation (i.e. they are aligned quite close to the circumferential direction). By contrast, in the adventitial and intimal layers, the orientation of the collagen fibres is dispersed, as shown by polarized light microscopy of stained arterial tissue. As a result, continuum models that do not account for the dispersion are not able to capture accurately the stress-strain response of these layers. The purpose of this paper, therefore, is to develop a structural continuum framework that is able to represent the dispersion of the collagen fibre orientation. This then allows the development of a new hyperelastic free-energy function that is particularly suited for representing the anisotropic elastic properties of adventitial and intimal layers of arterial walls, and is a generalization of the fibre-reinforced structural model introduced by Holzapfel & Gasser (Holzapfel & Gasser 2001 Comput. Meth. Appl. Mech. Eng. 190, 4379-4403) and Holzapfel et al. (Holzapfel et al. 2000 J. Elast. 61, 1-48). The model incorporates an additional scalar structure parameter that characterizes the dispersed collagen orientation. An efficient finite element implementation of the model is then presented and numerical examples show that the dispersion of the orientation of collagen fibres in the adventitia of human iliac arteries has a significant effect on their mechanical response.
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| 3. |
- Gerlee, Philip, 1980, et al.
(author)
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Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms
- 2009
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 6, s. 1233-1245
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Journal article (peer-reviewed)abstract
- We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.
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| 4. |
- Hedenström, Anders, et al.
(author)
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Beyond robins: aerodynamic analyses of animal flight.
- 2008
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 5:23, s. 595-601
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Journal article (peer-reviewed)abstract
- Recent progress in studies of animal flight mechanics is reviewed. A range of birds, and now bats, has been studied in wind tunnel facilities, revealing an array of wake patterns caused by the beating wings and also by the drag on the body. Nevertheless, the quantitative analysis of these complex wake structures shows a degree of similarity among all the different wake patterns and a close agreement with standard quasi-steady aerodynamic models and predictions. At the same time, new data on the flow over a bat wing in mid-downstroke show that, at least in this case, such simplifications cannot be useful in describing in detail either the wing properties or control prospects. The reasons for these apparently divergent results are discussed and prospects for future advances are considered.
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| 5. |
- Hedenström, Anders, et al.
(author)
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Vortex wakes generated by robins Erithacus rubecula during free flight in a wind tunnel
- 2006
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 3:7, s. 263-276
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Journal article (peer-reviewed)abstract
- The wakes of two individual robins were measured in digital particle image velocimetry (DPIV) experiments conducted in the Lund wind tunnel. Wake measurements were compared with each other, and with previous studies in the same facility. There was no significant individual variation in any of the measured quantities. Qualitatively, the wake structure and its gradual variation with flight speed were exactly as previously measured for the thrush nightingale. A procedure that accounts for the disparate sources of circulation spread over the complex wake structure nevertheless can account for the vertical momentum flux required to support the weight, and an example calculation is given for estimating drag from the components of horizontal momentum flux (whose net value is zero). The measured circulations of the largest structures in the wake can be predicted quite well by simple models, and expressions are given to predict these and other measurable quantities in future bird flight experiments.
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| 6. |
- Holme, Petter
(author)
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Model validation of simple-graph representations of metabolism
- 2009
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 6:40, s. 1027-1034
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Journal article (peer-reviewed)abstract
- The large-scale properties of chemical reaction systems, such as metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information, lists of chemical reactions, available in databases. Even for the simplest type of graph representation, this reduction can be done in several ways. We investigate different simple network representations by testing how well they encode information about one biologically important network structure-network modularity (the propensity for edges to be clustered into dense groups that are sparsely connected between each other). To achieve this goal, we design a model of reaction systems where network modularity can be controlled and measure how well the reduction to simple graphs captures the modular structure of the model reaction system. We find that the network types that best capture the modular structure of the reaction system are substrate-product networks (where substrates are linked to products of a reaction) and substance networks (with edges between all substances participating in a reaction). Furthermore, we argue that the proposed model for reaction systems with tunable clustering is a general framework for studies of how reaction systems are affected by modularity. To this end, we investigate statistical properties of the model and find, among other things, that it recreates correlations between degree and mass of the molecules.
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| 7. |
- Holme, Petter, et al.
(author)
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Role-similarity based functional prediction in networked systems : application to the yeast proteome
- 2005
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 2:4, s. 327-333
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Journal article (peer-reviewed)abstract
- We propose a general method to predict functions of vertices where (i) the wiring of the network is somehow related to the vertex functionality and (ii) a fraction of the vertices are functionally classified. The method is influenced by role-similarity measures of social network analysis. The two versions of our prediction scheme axe tested on model networks where the functions of the vertices are designed to match their network surroundings. We also apply these methods to the proteome of the yeast Saccharomyces cerevisiae and find the results compatible with more specialized methods.
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| 8. |
- Rosén, Mikael, et al.
(author)
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Wake structure and wingbeat kinematics of a house-martin Delichon urbica
- 2007
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 4:15, s. 659-668
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Journal article (peer-reviewed)abstract
- The wingbeat kinematics and wake structure of a trained house martin in free, steady flight in a wind tunnel have been studied over a range of flight speeds, and compared and contrasted with similar measurements for a thrush nightingale and a pair of robins. The house martin has a higher aspect ratio (more slender) wing, and is a more obviously agile and aerobatic flyer, catching insects on the wing. The wingbeat is notable for the presence at higher flight speeds of a characteristic pause in the upstroke. The essential characteristics of the wing motions can be reconstructed with a simple two-frequency model derived from Fourier analysis. At slow speeds, the distribution of wake vorticity is more simple than for the other previously measured birds, and the upstroke does not contribute to weight support. The upstroke becomes gradually more significant as the flight speed increases, and although the vortex wake shows a signature of the pause phase, the global circulation measurements are otherwise in good agreement with surprisingly simple aerodynamic models, and with predictions across the different species, implying quite similar aerodynamic performance of the wing sections. The local Reynolds numbers of the wing sections are sufficiently low that the well-known instabilities of attached laminar flows over lifting surfaces, which are known to occur at two to three times this value, may not develop.
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| 9. |
- Salfity, M.F., et al.
(author)
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Extending the dynamic range of phase contrast magnetic resonance velocity imaging using advanced higher-dimensional phase unwrapping algorithms
- 2006
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:8, s. 415-427
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Journal article (peer-reviewed)abstract
- Phase contrast magnetic resonance velocity imaging is a powerful technique for quantitative in vivo blood flow measurement. Current practice normally involves restricting the sensitivity of the technique so as to avoid the problem of the measured phase being 'wrapped' onto the range - π to + π. However, as a result, dynamic range and signal-to-noise ratio are sacrificed. Alternatively, the true phase values can be estimated by a phase unwrapping process which consists of adding integral multiples of 2π to the measured wrapped phase values. In the presence of noise and data undersampling, the phase unwrapping problem becomes non-trivial. In this paper, we investigate the performance of three different phase unwrapping algorithms when applied to three-dimensional (two spatial axes and one time axis) phase contrast datasets. A simple one-dimensional temporal unwrapping algorithm, a more complex and robust three-dimensional unwrapping algorithm and a novel velocity encoding unwrapping algorithm which involves unwrapping along a fourth dimension (the 'velocity encoding' direction) are discussed, and results from the three are presented and compared. It is shown that compared to the traditional approach, both dynamic range and signal-to-noise ratio can be increased by a factor of up to five times, which demonstrates considerable promise for a possible eventual clinical implementation. The results are also of direct relevance to users of any other technique delivering time-varying two-dimensional phase images, such as dynamic speckle interferometry and synthetic aperture radar
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