Optical design of two-reflector systems, the Monge-Kantorovich mass transfer problem and Fermat's principle

It is shown that the problem of designing a two-reflector system transforming a plane wave front with given intensity into an output plane front with prescribed output intensity can be formulated and solved as the Monge-Kantorovich mass transfer problem.Comment: 25 pages, 2 figure

Modeling the Interplay of Oscillatory Synchronization and Aggregation via Cell-Cell Adhesion

We present a model of systems of cells with intracellular oscillators ('clocks'). This is motivated by examples from developmental biology and from the behavior of organisms on the threshold to multicellularity. Cells undergo random motion and adhere to each other. The adhesion strength between neighbors depends on their clock phases in addition to a constant baseline strength. The oscillators are linked via Kuramoto-type local interactions. The model is an advection-diffusion partial differential equation with nonlocal advection terms. We demonstrate that synchronized states correspond to Dirac-delta measure solutions of a weak version of the equation. To analyze the complex interplay of aggregation and synchronization, we then perform a linear stability analysis of the incoherent, spatially uniform state. This lets us classify possibly emerging patterns depending on model parameters. Combining these results with numerical simulations, we determine a range of possible far-from equilibrium patterns when baseline adhesion strength is zero: There is aggregation into separate synchronized clusters with or without global synchrony; global synchronization without aggregation; or unexpectedly a ``phase wave" pattern characterized by spatial gradients of clock phases. A 2D Lattice-Gas Cellular Automaton model confirms and illustrates these results

Isolating and Quantifying the Role of Developmental Noise in Generating Phenotypic Variation

Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to intrinsic mechanisms within organisms that stabilize phenotypes and decrease variation. Since we are just beginning to appreciate the extent to which phenotypic variation due to stochasticity is potentially adaptive, the contribution of developmental noise to phenotypic variation must be separated and measured to fully understand its role in evolution. Here, we show that variation in the component of the developmental process corresponding to environmental and genetic factors (here treated together as a unit called the LALI-type) versus the contribution of developmental noise, can be distinguished for leopard gecko (Eublepharis macularius) head color patterns using mathematical simulations that model the role of random variation (corresponding to developmental noise) in patterning. Specifically, we modified the parameters of simulations corresponding to variation in the LALI-type to generate the full range of phenotypic variation in color pattern seen on the heads of eight leopard geckos. We observed that over the range of these parameters, variation in color pattern due to LALI-type variation exceeds that due to developmental noise in the studied gecko cohort. However, the effect of developmental noise on patterning is also substantial. Our approach addresses one of the major goals of evolutionary biology: to quantify the role of stochasticity in shaping phenotypic variation

On Isoconcentration Surfaces of Three Dimensional Turing Patterns

We consider three-dimensional Turing patterns and their isoconcentration surfaces corresponding to the equilibrium concentration of the reaction kinetics. We call these surfaces equilibrium concentration surfaces (EC surfaces). They are the interfaces between the regions of high and low concentrations in Turing patterns. We give alternate characterizations of EC surfaces by means of two variational principles, one of them being that they are optimal for diffusive transport. Several examples of EC surfaces are considered. Remarkably, they are often very well approximated by certain minimal surfaces. We give a dynamical explanation for the emergence of Scherk\u27s surface in certain cases, a structure that has been observed numerically previously in [De Wit et al., 1997]

On the Supersymmetry Group of the Classical Bose-Fermi Oscillator,

Applying the concept of a momentum map for supersymplectic supervectorspaces to the one-dimensional Bose-Fermi oscillator, we show that the largest symmetry group that admits a momentum map is the identity component of the intersection of the orthosymplectic group OSp(2|2) and the group of supersymplectic transformations. This gives a systematic characterization of a certain class of odd supersymmetry transformations that were originally introduced in an ad hoc way

Iterative Scheme for Solving Optimal Transportation Problems Arising in Reflector Design

We consider the geometric optics problem of finding a system of two reflectors that transform a spherical wavefront into a beam of parallel rays with prescribed intensity distribution. Using techniques from optimal transportation theory, it has been shown previously that this problem is equivalent to an infinite-dimensional linear programming (LP) problem. Here we investigate techniques for constructing the two reflectors numerically by considering the finite dimensional LP problems which arise as approximations to the infinite dimensional problem. A straightforward discretization has the disadvantage that the number of constraints increases rapidly with the mesh size, so only very coarse meshes are practical. To address this well-known issue we propose an iterative solution scheme. In each step an LP problem is solved, where information from the previous iteration step is used to reduce the number of necessary constraints. As an illustration we apply our proposed scheme to solve a problem with synthetic data, demonstrating that the method allows for much finer meshes than a simple discretization. We also give evidence that the scheme converges. There exists a growing literature for the application of optimal transportation theory to other beam shaping problems, and our proposed scheme is easy to adapt for these problems as well

A rigorous analysis using optimal transport theory for a two-reflector design problem with a point source

We consider the following geometric optics problem: Construct a system of two reflectors which transforms a spherical wavefront generated by a point source into a beam of parallel rays. This beam has a prescribed intensity distribution. We give a rigorous analysis of this problem. The reflectors we construct are (parts of) the boundaries of convex sets. We prove existence of solutions for a large class of input data and give a uniqueness result. To the author's knowledge, this is the first time that a rigorous mathematical analysis of this problem is given. The approach is based on optimal transportation theory. It yields a practical algorithm for finding the reflectors. Namely, the problem is equivalent to a constrained linear optimization problem.Comment: 5 Figures - pdf files attached to submission, but not shown in manuscrip

Deep Phylogenomics of a Tandem-Repeat Galectin Regulating Appendicular Skeletal Pattern Formation

BACKGROUND: A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern. RESULTS: Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection. CONCLUSION: These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods

The Morphostatic Limit for a Model of Skeletal Pattern Formation in the Vertebrate Limb

A recently proposed mathematical model of a “core” set of cellular and molecular interactions present in the developing vertebrate limb was shown to exhibit pattern-forming instabilities and limb skeleton-like patterns under certain restrictive conditions, suggesting that it may authentically represent the underlying embryonic process (Hentschel et al., Proc. R. Soc. B 271, 1713–1722,2004). The model, an eight-equation system of partial differential equations, incorporates the behavior of mesenchymal cells as “reactors,” both participating in the generation of morphogen patterns and changing their state and position in response to them. The full system, which has smooth solutions that exist globally in time, is nonetheless highly complex and difficult to handle analytically or numerically. According to a recent classification of developmental mechanisms (Salazar-Ciudad et al., Development 130, 2027–2037, 2003), the limb model of Hentschel et al. is “morphodynamic,” since differentiation of new cell types occurs simultaneously with cell rearrangement. This contrasts with “morphostatic” mechanisms, in which cell identity becomes established independently of cell rearrangement. Under the hypothesis that development of some vertebrate limbs employs the core mechanism in a morphostatic fashion, we derive in an analytically rigorous fashion a pair of equations representing the spatiotemporal evolution of the morphogen fields under the assumption that cell differentiation relaxes faster than the evolution of the overall cell density (i.e., the morphostatic limit of the full system). This simple reaction–diffusion system is unique in having been derived analytically from a substantially more complex system involving multiple morphogens, extracellular matrix deposition, haptotaxis, and cell translocation. We identify regions in the parameter space of the reduced system where Turing-type pattern formation is possible, which we refer to as its “Turing space.” Obtained values of the parameters are used in numerical simulations of the reduced system, using a new Galerkin finite element method, in tissue domains with nonstandard geometry. The reduced system exhibits patterns of spots and stripes like those seen in developing limbs, indicating its potential utility in hybrid continuum-discrete stochastic modeling of limb development. Lastly, we discuss the possible role in limb evolution of selection for increasingly morphostatic developmental mechanisms