Limitations of field-theory simulation for exploring phase separation: The role of repulsion in a lattice protein model.

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.

Optical advantages and function of multifocal spherical fish lenses.

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.

Regulated transport as a mechanism for pattern generation: capabilities for phyllotaxis and beyond.

Large-scale pattern formation is a frequently occurring phenomenon in biological organisms, and several local interaction rules for generating such patterns have been suggested. A mechanism driven by feedback between the plant hormone auxin and its polarly localized transport mediator PINFORMED1 has been proposed as a model for phyllotactic patterns in plants. It has been shown to agree with current biological experiments at a molecular level as well as with respect to the resulting patterns. We present a thorough investigation of variants of models based on auxin-regulated polarized transport and use analytical and numerical tools to derive requirements for these models to drive spontaneous pattern formation. We find that auxin concentrations in neighboring cells can feed back either on exocytosis or endocytosis and still produce patterns. In agreement with mutant experiments, the active cellular efflux is shown to be more important for pattern capabilities as compared to active influx. We also find that the feedback must originate from neighboring cells rather than from neighboring walls and that intracellular competition for the transport mediator is required for patterning. The importance of model parameters is investigated, especially regarding robustness to perturbations of experimentally estimated parameter values. Finally, the regulated transport mechanism is shown to be able to generate Turing patterns of various types.

An approximate maximum likelihood approach, applied to phylogenetic trees.

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 approximation, 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.

General formalism for inhomogeneous random graphs.

We present and investigate an extension of the classical random graph to a general class of inhomogeneous random graph models, where vertices come in different types, and the probability of realizing an edge depends on the types of its terminal vertices. This approach provides a general framework for the analysis of a large class of models. The generic phase structure is derived using generating function techniques, and relations to other classes of models are pointed out.

Properties of random graphs with hidden color.

We investigate in some detail a recently suggested general class of ensembles of sparse undirected random graphs based on a hidden stub coloring, with or without the restriction to nondegenerate graphs. The calculability of local and global structural properties of graphs from the resulting ensembles is demonstrated. Cluster size statistics are derived with generating function techniques, yielding a well-defined percolation threshold. Explicit rules are derived for the enumeration of small subgraphs. Duality and redundancy is discussed, and subclasses corresponding to commonly studied models are identified.

Random graphs with hidden color.

We propose and investigate a unifying class of sparse random graph models, based on a hidden coloring of edge-vertex incidences, extending an existing approach, random graphs with a given degree distribution, in a way that admits a nontrivial correlation structure in the resulting graphs. The approach unifies a number of existing random graph ensembles within a common general formalism, and allows for the analytic calculation of observable graph characteristics. In particular, generating function techniques are used to derive the size distribution of connected components (clusters) as well as the location of the percolation threshold where a giant component appears.

Perturbative solution to susceptible-infected-susceptible epidemics on networks.

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.

Adjusting a light dispersion model to fit measurements from vertebrate ocular media as well as ray-tracing in fish lenses.

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.

Effects of the peripheral layers on the optical properties of spherical fish lenses.

We created a computational optical model of spherical fish lenses that takes into account the effects of the peripheral layers, which 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 be set by the metabolic needs of the lens.

Improved algorithm for simulations of divergent-light halos.

Divergent-light halos are produced when light from nearby light sources is scattered by ice crystals in the atmosphere. We present a theory of divergent-light halos leading to an improved algorithm for the simulation of such halos. Contrary to the algorithm that we presented earlier for simulating such halos, the new algorithm includes a mathematically rigorous weighting of the events. The computer implementation is very compact, and the whole procedure is elegant and conceptually easy to understand. We also present a new simulation atlas showing halos produced by crystals of different shapes and orientations for a set of elevations of the light source.