| 1. |
- Gagnon, Yakir, et al.
(författare)
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Adjusting a light dispersion model to fit measurements from vertebrate ocular media as well as ray-tracing in fish lenses.
- 2010
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Ingår i: Vision Research. - : Elsevier BV. - 1878-5646 .- 0042-6989. ; 50:9, s. 850-853
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Tidskriftsartikel (refereegranskat)abstract
- Color dispersion, i.e., the dependency of refractive index of any transparent material on the wavelength of light, has important consequences for the function of optical instruments and animal eyes. Using a multi-objective goal attainment optimization algorithm, a dispersion model was successfully fitted to measured refractive indices of various ocular media and the longitudinal chromatic aberration determined by laser-scanning in the crystalline lens of the African cichlid fish, Astatotilapia burtoni. The model describes the effects of color dispersion in fish lenses and may be applicable to the eyes of other vertebrates as well.
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| 2. |
- Gagnon, Yakir, et al.
(författare)
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Effects of the peripheral layers on the optical properties of spherical fish lenses
- 2008
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Ingår i: Journal of the Optical Society of America A. - 1084-7529. ; 25:10, s. 2468-2475
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Tidskriftsartikel (refereegranskat)abstract
- We created a computational optical model of spherical fish lenses that takes into account the effects of the peripheral layers that differ in cellular composition from the bulk of the lens. A constant refractive index, except for the lens capsule, in the outer about 6 % of lens radius made it possible to uniquely infer the refractive index gradient in more central layers from a known or desired longitudinal spherical aberration curve using the inverse Abel transform. Since the zone of constant refractive index is wider than necessary to make the solution unique and for optimal optical performance of the lens, we propose that its width is set by the metabolic needs of the lens.
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| 3. |
- Gagnon, Yakir, et al.
(författare)
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Optical advantages and function of multifocal spherical fish lenses
- 2012
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Ingår i: Journal of the Optical Society of America A. - 1084-7529. ; 29:9, s. 1786-1793
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Tidskriftsartikel (refereegranskat)abstract
- The spherical crystalline lenses in the eyes of many fish species are well-suited models for studies on how natural selection has influenced the evolution of the optical system. Many of these lenses exhibit multiple focal lengths when illuminated with monochromatic light. Similar multifocality is present in a majority of vertebrate eyes, and it is assumed to compensate for the defocusing effect of longitudinal chromatic aberration. In order to identify potential optical advantages of multifocal lenses, we studied their information transfer capacity by computer modeling. We investigated four lens types: the lens of Astatotilapia burtoni, an African cichlid fish species, an equivalent monofocal lens, and two artificial multifocal lenses. These lenses were combined with three detector arrays of different spectral properties: the cone photoreceptor system of A. burtoni and two artificial arrays. The optical properties compared between the lenses were longitudinal spherical aberration curves, point spread functions, modulation transfer functions, and imaging characteristics. The multifocal lenses had a better balance between spatial and spectral information than the monofocal lenses. Additionally, the lens and detector array had to be matched to each other for optimal function. (C) 2012 Optical Society of America
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| 4. |
- Nilsson, Daniel, et al.
(författare)
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Limitations of field-theory simulation for exploring phase separation: The role of repulsion in a lattice protein model
- 2022
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Ingår i: The Journal of chemical physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 156:1
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Tidskriftsartikel (refereegranskat)abstract
- Field-theory simulation by the complex Langevin method offers an alternative to conventional sampling techniques for exploring the forces driving biomolecular liquid–liquid phase separation. Such simulations have recently been used to study several polyampholyte systems. Here, we formulate a field theory corresponding to the hydrophobic/polar (HP) lattice protein model, with finite same-site repulsion and nearest-neighbor attraction between HH bead pairs. By direct comparison with particle-based Monte Carlo simulations, we show that complex Langevin sampling of the field theory reproduces the thermodynamic properties of the HP model only if the same-site repulsion is not too strong. Unfortunately, the repulsion has to be taken weaker than what is needed to prevent condensed droplets from assuming an artificially compact shape. Analysis of a minimal and analytically solvable toy model hints that the sampling problems caused by repulsive interaction may stem from loss of ergodicity.
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| 5. |
- Pigeon, Simon, et al.
(författare)
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Tracer particle diffusion in a system with hardcore interacting particles
- 2017
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Ingår i: Journal of Statistical Mechanics: Theory and Experiment. - : IOP Publishing. - 1742-5468. ; 2017:12
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Tidskriftsartikel (refereegranskat)abstract
- In this study, inspired by the work of Nakazato and Kitahara (1980 Prog. Theor. Phys. 64 2261), we consider the theoretical problem of tracer particle diffusion in an environment of diffusing hardcore interacting crowder particles. The tracer particle has a different diffusion constant from the crowder particles. Based on a transformation of the generating function, we provide an exact formal expansion for the tracer particle probability density, valid for any lattice in the thermodynamic limit. By applying this formal solution to dynamics on a regular Bravais lattice we provide a closed form approximation for the tracer particle diffusion constant which extends the Nakazato and Kitahara results to include also b.c.c. and f.c.c. lattices. Finally, we compare our analytical results to simulations in two and three dimensions.
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| 6. |
- Sanders, Lloyd, et al.
(författare)
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Perturbative solution to susceptible-infected-susceptible epidemics on networks.
- 2013
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Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755. ; 88:3
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Tidskriftsartikel (refereegranskat)abstract
- Herein we provide a closed form perturbative solution to a general M-node network susceptible-infected-susceptible (SIS) model using the transport rates between nodes as a perturbation parameter. We separate the dynamics into a short-time regime and a medium-to-long-time regime. We solve the short-time dynamics of the system and provide a limit before which our explicit, analytical result of the first-order perturbation for the medium-to-long-time regime is to be employed. These stitched calculations provide an approximation to the full temporal dynamics for rather general initial conditions. To further corroborate our results, we solve the mean-field equations numerically for an infectious SIS outbreak in New Zealand (NZ, Aotearoa) recomposed into 23 subpopulations where the virus is spread to different subpopulations via (documented) air traffic data, and the country is internationally quarantined. We demonstrate that our analytical predictions compare well to the numerical solution.
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| 7. |
- Galvanovskis, Juris, et al.
(författare)
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Probability of Exocytosis in Pancreatic β-Cells : Dependence on Ca2+ Sensing Latency Times, Ca2+ Channel Kinetic Parameters, and Channel Clustering
- 2008
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Ingår i: Biosimulation in Drug Development. - Weinheim, Germany : Wiley-VCH Verlag GmbH & Co. KGaA. - 9783527316991 ; , s. 299-311
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Bokkapitel (refereegranskat)abstract
- The fusion of secretory vesicles and granules with the cell membrane prior to the release of their content into the extracellular space requires a transient increase of free Ca2+ concentration in the vicinity of the fusion site. Usually there is a short temporal delay in the onset of the actual fusion of membranes with reference to the rising free Ca2+ levels. This delay is described as a latency time of the Ca2+-sensing system of the secretory machinery and has been observed in several cell types, including pancreatic β-cells. The presence of a delay time of a finite length inherent to the secretory machinery of the cell has an essential effect on the probability for a certain granule to fuse with the cell membrane and to release its contents into the extracellular space during the action potential. We investigate here, theoretically and by numerical simulations, the extent of this influence and its dependence on the parameters of Ca2+ channels, channel clustering, the Ca2+-sensing system, and the length of depolarizing pulses.We use a linear probabilistic model for a random opening and closing of channels that yields an explicit expression for the Laplace transforms of the waiting time distributions for an event that at least one channel is open during the latency time. This allows one in principle to calculate the probability that a vesicle will fuse with the cell membrane during the action potential. We compare our theoretical results with numerical simulatio
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| 8. |
- Jönsson, Henrik, et al.
(författare)
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An approximate maximum likelihood approach, applied to phylogenetic trees
- 2003
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Ingår i: Journal of Computational Biology. - 1557-8666. ; 10:5, s. 737-749
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Tidskriftsartikel (refereegranskat)abstract
- A novel type of approximation scheme to the maximum likelihood (ML) approach is presented and discussed in the context of phylogenetic tree reconstruction from aligned DNA sequences. It is based on a parameterized approximation to the conditional distribution of hidden variables (related, e.g., to the sequences of unobserved branch point ancestors) given the observed data. A modified likelihood, based on the extended data, is then maximized with respect to the parameters of the model as well as to those involved in the approximation. With a suitable form of the approximations the proposed method allows for simpler updating of the parameters, at the cost of an increased parameter count and a slight decrease in performance. The method is tested on phylogenetic tree reconstruction from artificially generated sequences, and its performance is compared to that of ML, showing that the approach is competitive for reasonably similar sequences. The method is also applied to real DNA sequences from primates, yielding a result consistent with those obtained by other standard algorithms.
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| 9. |
- Jönsson, Henrik, et al.
(författare)
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An information-based neural approach to generic constraint satisfaction
- 2002
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Ingår i: Artificial Intelligence. - 1872-7921. ; 142:1, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- A novel artificial neural network heuristic (INN) for general constraint satisfaction problems is presented. extending a recently suggested method restricted to boolean variables. In contrast to conventional ANN methods, it employs a particular type of non-polynomial cost function, based on the information balance between variables and constraints in a mean-field setting. Implemented as an annealing algorithm, the method is numerically explored on a testbed of Graph Coloring problems. The performance is comparable to that of dedicated heuristics, and clearly superior to that of conventional mean-field annealing.
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| 10. |
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