| 1. |
- Andric, Jelena, 1979, et al.
(författare)
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A study of a flexible fiber model and its behavior in DNS of turbulent channel flow
- 2013
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Ingår i: Acta Mechanica. - : Springer Science and Business Media LLC. - 0001-5970 .- 1619-6937. ; 224:10, s. 2359-2374
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Tidskriftsartikel (refereegranskat)abstract
- The dynamics of individual flexible fibers in a turbulent flow field have been analyzed, varying their initial position, density and length. A particlelevel fiber model has been integrated into a general-purpose, open source Computational Fluid Dynamics (CFD) code. The fibers are modeled as chains of cylindrical segments connected by ball and socket joints. The equations of motion of the fibers contain the inertia of the segments, the contributions from hydrodynamic forces and torques, and the connectivity forces at the joints. Direct Numerical Simulation (DNS) of the incompressible Navier–Stokes equations is used to describe the fluid flow in a plane channel and a one-way coupling is considered between the fibers and the fluid phase. We investigate the translational motion of fibers by considering the mean square displacement of their trajectories. We find that the fiber motion is primarily governed by velocity correlations of the flow fluctuations. In addition, we show that there is a clear tendency of the thread-like fibers to evolve into complex geometrical configurations in a turbulent flow field, in fashion similar to random conformations of polymer strands subjected to thermal fluctuations in a suspension. Finally, we show that fiber inertia has a significant impact on reorientation time-scales of fibers suspended in a turbulent flow field.
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| 2. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
- 2019
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 2019:2
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Tidskriftsartikel (refereegranskat)abstract
- Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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| 3. |
- Asadzadeh, Mohammad, 1952, et al.
(författare)
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Convergence of Finite Volume Scheme for a Three-Dimensional Poisson Equation
- 2014
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Ingår i: Journal of Mathematical Sciences. - : Springer-Verlag New York. - 1072-3374 .- 1573-8795. ; 202:2, s. 130-153
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Tidskriftsartikel (refereegranskat)abstract
- We construct and analyze a finite volume scheme for numerical solution of a three-dimensional Poisson equation. We derive optimal convergence rates in the discrete H1 norm and sub-optimal convergence in the maximum norm, where we use the maximal available regularity of the exact solution and minimal smoothness requirement on the source term. The theoretical results are justified through implementing some canonical examples in 3D.
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| 4. |
- Bally, Marta, 1981, et al.
(författare)
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Interaction of Single Viruslike Particles with Vesicles Containing Glycosphingolipids
- 2011
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 107:18
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Tidskriftsartikel (refereegranskat)abstract
- Glycosphingolipids are involved in the first steps of virus-cell interaction, where they mediate specific recognition of the host cell membrane. We have employed total-internal-reflection fluorescence microscopy to explore the interaction kinetics between individual unlabeled noroviruslike particles, which are attached to a glycosphingolipid-containing lipid bilayer, and fluorescent vesicles containing different types and concentrations of glycosphingolipids. Under association equilibrium, the vesicle-binding rate is found to be kinetically limited, yielding information on the corresponding activation energy. The dissociation kinetics are logarithmic over a wide range of time. The latter is explained by the vesicle-size-related distribution of the dissociation activation energy. The biological, pharmaceutical, and diagnostic relevance of the study is briefly discussed.
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| 5. |
- Bally, Marta, 1981, et al.
(författare)
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Norovirus GII.4 Virus-like Particles Recognize Galactosylceramides in Domains of Planar Supported Lipid Bilayers.
- 2012
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 51:48, s. 12020-4
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Tidskriftsartikel (refereegranskat)abstract
- A sticky situation: Domain-dependent recognition of the glycosphingolipid galactosylceramide by norovirus-like particles (see picture; red/yellow) is shown using supported lipid bilayers (purple) as model membranes. Optimal ligand presentation is found to promote strong binding to GalCer. This presentation can be found at the edges of the glycosphingolipid-enriched domains (green) and binding is repressed in the absence of these domains.
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| 6. |
- Barrenäs, Fredrik, et al.
(författare)
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Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms
- 2012
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Ingår i: Genome Biology. - : BioMed Central. - 1465-6906 .- 1474-760X .- 1465-6914. ; 13:6, s. R46-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Complex diseases are associated with altered interactions between thousands of genes. We developed a novel method to identify and prioritize disease genes, which was generally applicable to complex diseases.RESULTS: We identified modules of highly interconnected genes in disease-specific networks derived from integrating gene-expression and protein interaction data. We examined if those modules were enriched for disease-associated SNPs, and could be used to find novel genes for functional studies. First, we analyzed publicly available gene expression microarray and genome-wide association study (GWAS) data from 13, highly diverse, complex diseases. In each disease, highly interconnected genes formed modules, which were significantly enriched for genes harboring disease-associated SNPs. To test if such modules could be used to find novel genes for functional studies, we repeated the analyses using our own gene expression microarray and GWAS data from seasonal allergic rhinitis. We identified a novel gene, FGF2, whose relevance was supported by functional studies using combined small interfering RNA-mediated knock-down and gene expression microarrays. The modules in the 13 complex diseases analyzed here tended to overlap and were enriched for pathways related to oncological, metabolic and inflammatory diseases. This suggested that this union of the modules would be associated with a general increase in susceptibility for complex diseases. Indeed, we found that this union was enriched with GWAS genes for 145 other complex diseases.CONCLUSIONS: Modules of highly interconnected complex disease genes were enriched for disease-associated SNPs, and could be used to find novel genes for functional studies.
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| 7. |
- Bartoszek, Krzysztof, et al.
(författare)
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A consistent estimator of the evolutionary rate
- 2015
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
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Tidskriftsartikel (refereegranskat)abstract
- We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.
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| 8. |
- Bartoszek, Krzysztof, 1984, et al.
(författare)
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A phylogenetic comparative method for studying multivariate adaptation
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 204-215
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptation between traits. Based on Ornstein–Uhlenbeck (OU) models of adaptive evolution, we present a method, with R implementation, in which multiple traits evolve both in response to each other and, as in previous OU models, to fixed or randomly evolving predictor variables. We present the interpretation of the model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antler and body-size evolution in deer (Cervidae).
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| 9. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Critical case stochastic phylogenetic tree model via the Laplace transform
- 2014
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Ingår i: Demonstratio Matematicae. - : De Gruyter. - 0420-1213 .- 2391-4661. ; 47:2, s. 474-481
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Tidskriftsartikel (refereegranskat)abstract
- Birth-and-death models are now a common mathematical tool to describe branching patterns observed in real-world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth-and-death model that is compatible with phylogenetic trees of both in uenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the death rate. This is a non-trivial situation and to study its asymptotic behaviour we employed the Laplace transform. With this we correct the proof of Liggett and Schinazi (2009) in the critical case.
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| 10. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Phylogenetic confidence intervals for the optimal trait value
- 2015
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Ingår i: Journal of Applied Probability. - : Cambridge University Press (CUP). - 0021-9002 .- 1475-6072. ; 52:4, s. 1115-1132
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Tidskriftsartikel (refereegranskat)abstract
- We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.
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