Turing conditions for pattern forming systems on evolving manifolds

The study of pattern-forming instabilities in reaction-diffusion systems on growing or otherwise time-dependent domains arises in a variety of settings, including applications in developmental biology, spatial ecology, and experimental chemistry. Analyzing such instabilities is complicated, as there is a strong dependence of any spatially homogeneous base states on time, and the resulting structure of the linearized perturbations used to determine the onset of instability is inherently non-autonomous. We obtain general conditions for the onset and structure of diffusion driven instabilities in reaction-diffusion systems on domains which evolve in time, in terms of the time-evolution of the Laplace-Beltrami spectrum for the domain and functions which specify the domain evolution. Our results give sufficient conditions for diffusive instabilities phrased in terms of differential inequalities which are both versatile and straightforward to implement, despite the generality of the studied problem. These conditions generalize a large number of results known in the literature, such as the algebraic inequalities commonly used as a sufficient criterion for the Turing instability on static domains, and approximate asymptotic results valid for specific types of growth, or specific domains. We demonstrate our general Turing conditions on a variety of domains with different evolution laws, and in particular show how insight can be gained even when the domain changes rapidly in time, or when the homogeneous state is oscillatory, such as in the case of Turing-Hopf instabilities. Extensions to higher-order spatial systems are also included as a way of demonstrating the generality of the approach

Bifurcations and dynamics emergent from lattice and continuum models of bioactive porous media

We study dynamics emergent from a two-dimensional reaction--diffusion process modelled via a finite lattice dynamical system, as well as an analogous PDE system, involving spatially nonlocal interactions. These models govern the evolution of cells in a bioactive porous medium, with evolution of the local cell density depending on a coupled quasi--static fluid flow problem. We demonstrate differences emergent from the choice of a discrete lattice or a continuum for the spatial domain of such a process. We find long--time oscillations and steady states in cell density in both lattice and continuum models, but that the continuum model only exhibits solutions with vertical symmetry, independent of initial data, whereas the finite lattice admits asymmetric oscillations and steady states arising from symmetry-breaking bifurcations. We conjecture that it is the structure of the finite lattice which allows for more complicated asymmetric dynamics. Our analysis suggests that the origin of both types of oscillations is a nonlocal reaction-diffusion mechanism mediated by quasi-static fluid flow.Comment: 30 pages, 21 figure

Amplitude death criteria for coupled complex Ginzburg-Landau systems

Amplitude death, which occurs in a system when one or more macroscopic wavefunctions collapse to zero, has been observed in mutually coupled solid-state lasers, analog circuits, and thermoacoustic oscillators, to name a few applications. While studies have considered amplitude death on oscillator systems and in externally forced complex Ginzburg-Landau systems, a route to amplitude death has not been studied in autonomous continuum systems. We derive simple analytic conditions for the onset of amplitude death of one macroscopic wavefunction in a system of two coupled complex Ginzburg-Landau equations with general nonlinear self- and cross-interaction terms. Our results give a more general theoretical underpinning for recent amplitude death results reported in the literature, and suggest an approach for tuning parameters in such systems so that they either permit or prohibit amplitude death of a wavefunction (depending on the application). Numerical simulation of the coupled complex Ginzburg-Landau equations, for examples including cubic, cubic-quintic, and saturable nonlinearities, is used to illustrate the analytical results.Comment: 7 pages, 4 figure

Lattice and Continuum Modelling of a Bioactive Porous Tissue Scaffold

A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for tissue engineering applications make use of spatially homogeneous or spatially continuous equations to model cell growth, flow of culture medium, nutrient transport, and their interactions. The network structure of the physical porous scaffold is often incorporated through parameters in these models, either phenomenologically or through techniques like mathematical homogenization. We derive a model on a square grid lattice to demonstrate the importance of explicitly modelling the network structure of the porous scaffold, and compare results from this model with those from a modified continuum model from the literature. We capture two-way coupling between cell growth and fluid flow by allowing cells to block pores, and by allowing the shear stress of the fluid to affect cell growth and death. We explore a range of parameters for both models, and demonstrate quantitative and qualitative differences between predictions from each of these approaches, including spatial pattern formation and local oscillations in cell density present only in the lattice model. These differences suggest that for some parameter regimes, corresponding to specific cell types and scaffold geometries, the lattice model gives qualitatively different model predictions than typical continuum models. Our results inform model selection for bioactive porous tissue scaffolds, aiding in the development of successful tissue engineering experiments and eventually clinically successful technologies.Comment: 38 pages, 16 figures. This version includes a much-expanded introduction, and a new section on nonlinear diffusion in addition to polish throughou

Coupled complex Ginzburg-Landau systems with saturable nonlinearity and asymmetric cross-phase modulation

We formulate and study dynamics from a complex Ginzburg-Landau system with saturable nonlinearity, including asymmetric cross-phase modulation (XPM) parameters. Such equations can model phenomena described by complex Ginzburg-Landau systems under the added assumption of saturable media. When the saturation parameter is set to zero, we recover a general complex cubic Ginzburg-Landau system with XPM. We first derive conditions for the existence of bounded dynamics, approximating the absorbing set for solutions. We use this to then determine conditions for amplitude death of a single wavefunction. We also construct exact plane wave solutions, and determine conditions for their modulational instability. In a degenerate limit where dispersion and nonlinearity balance, we reduce our system to a saturable nonlinear Schr\"odinger system with XPM parameters, and we demonstrate the existence and behavior of spatially heterogeneous stationary solutions in this limit. Using numerical simulations we verify the aforementioned analytical results, while also demonstrating other interesting emergent features of the dynamics, such as spatiotemporal chaos in the presence of modulational instability. In other regimes, coherent patterns including uniform states or banded structures arise, corresponding to certain stable stationary states. For sufficiently large yet equal XPM parameters, we observe a segregation of wavefunctions into different regions of the spatial domain, while when XPM parameters are large and take different values, one wavefunction may decay to zero in finite time over the spatial domain (in agreement with the amplitude death predicted analytically). While saturation will often regularize the dynamics, such transient dynamics can still be observed - and in some cases even prolonged - as the saturability of the media is increased, as the saturation may act to slow the timescale.Comment: 36 page

Unstaggered-staggered solitons in two-component discrete nonlinear Schr\"{o}dinger lattices

We present stable bright solitons built of coupled unstaggered and staggered components in a symmetric system of two discrete nonlinear Schr\"{o}dinger (DNLS) equations with the attractive self-phase-modulation (SPM) nonlinearity, coupled by the repulsive cross-phase-modulation (XPM) interaction. These mixed modes are of a "symbiotic" type, as each component in isolation may only carry ordinary unstaggered solitons. The results are obtained in an analytical form, using the variational and Thomas-Fermi approximations (VA and TFA), and the generalized Vakhitov-Kolokolov (VK) criterion for the evaluation of the stability. The analytical predictions are verified against numerical results. Almost all the symbiotic solitons are predicted by the VA quite accurately, and are stable. Close to a boundary of the existence region of the solitons (which may feature several connected branches), there are broad solitons which are not well approximated by the VA, and are unstable

Unstaggered-staggered solitons on one- and two-dimensional two-component discrete nonlinear Schr\"{o}dinger lattices

We study coupled unstaggered-staggered soliton pairs emergent from a system of two coupled discrete nonlinear Schr\"{o}dinger (DNLS) equations with the self-attractive on-site self-phase-modulation nonlinearity, coupled by the repulsive cross-phase-modulation interaction, on 1D and 2D lattice domains. These mixed modes are of a "symbiotic" type, as each component in isolation may only carry ordinary unstaggered solitons. While most work on DNLS systems addressed symmetric on-site-centered fundamental solitons, these models give rise to a variety of other excited states, which may also be stable. The simplest among them are antisymmetric states in the form of discrete twisted solitons, which have no counterparts in the continuum limit. In the extension to 2D lattice domains, a natural counterpart of the twisted states are vortical solitons. We first introduce a variational approximation (VA) for the solitons, and then correct it numerically to construct exact stationary solutions, which are then used as initial conditions for simulations to check if the stationary states persist under time evolution. Two-component solutions obtained include (i) 1D fundamental-twisted and twisted-twisted soliton pairs, (ii) 2D fundamental-fundamental soliton pairs, and (iii) 2D vortical-vortical soliton pairs. We also highlight a variety of other transient dynamical regimes, such as breathers and amplitude death. The findings apply to modeling binary Bose-Einstein condensates, loaded in a deep lattice potential, with identical or different atomic masses of the two components, and arrays of bimodal optical waveguides.Comment: to be published in Communications in Nonlinear Science and Numerical Simulatio

Predator-prey-subsidy population dynamics on stepping-stone domains with dispersal delays

We examine the role of the travel time of a predator along a spatial network on predator-prey population interactions, where the predator is able to partially or fully sustain itself on a resource subsidy. The impact of access to food resources on the stability and behaviour of the predator-prey-subsidy system is investigated, with a primary focus on how incorporating travel time changes the dynamics. The population interactions are modelled by a system of delay differential equations, where travel time is incorporated as discrete delay in the network diffusion term in order to model time taken to migrate between spatial regions. The model is motivated by the Arctic ecosystem, where the Arctic fox consumes both hunted lemming and scavenged seal carcass. The fox travels out on sea ice, in addition to quadrennially migrating over substantial distances. We model the spatial predator-prey-subsidy dynamics through a “stepping-stone” approach. We find that a temporal delay alone does not push species into extinction, but rather may stabilize or destabilize coexistence equilibria. We are able to show that delay can stabilize quasi-periodic or chaotic dynamics, and conclude that the incorporation of dispersal delay has a regularizing effect on dynamics, suggesting that dispersal delay can be proposed as a solution to the paradox of enrichment

Measuring student attitude and knowledge in technology-rich biology classrooms

The use of technology in schools is now ubiquitous, but the effectiveness on the learning environment has mixed results. This paper describes the development and validation of an instrument to measure students’ attitudes toward and knowledge of technology with the aim of investigating any differences based on gender after a course where the science department made use of technology as an integral part of teaching biology. In this study, conducted in one school in the state of New York, in the United States of America, the Students’ Attitudes Toward and Knowledge of Technology Questionnaire was administered to nearly 700 high school science students. A principal component and principal factor analysis resulted in new scales from the validation of the instrument that demonstrated high reliabilities. There were statistically significant gender differences in all the scales of the questionnaire in favor of males