Hopf bifurcation from fronts in the Cahn-Hilliard equation

We study Hopf bifurcation from traveling-front solutions in the Cahn-Hilliard equation. The primary front is induced by a moving source term. Models of this form have been used to study a variety of physical phenomena, including pattern formation in chemical deposition and precipitation processes. Technically, we study bifurcation in the presence of essential spectrum. We contribute a simple and direct functional analytic method and determine bifurcation coefficients explicitly. Our approach uses exponential weights to recover Fredholm properties and spectral flow ideas to compute Fredholm indices. Simple mass conservation helps compensate for negative indices. We also construct an explicit, prototypical example, prove the existence of a bifurcating front, and determine the direction of bifurcation

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids.

During gastrulation, the pluripotent epiblast self-organizes into the 3 germ layers-endoderm, mesoderm and ectoderm, which eventually form the entire embryo. Decades of research in the mouse embryo have revealed that a signaling cascade involving the Bone Morphogenic Protein (BMP), WNT, and NODAL pathways is necessary for gastrulation. In vivo, WNT and NODAL ligands are expressed near the site of gastrulation in the posterior of the embryo, and knockout of these ligands leads to a failure to gastrulate. These data have led to the prevailing view that a signaling gradient in WNT and NODAL underlies patterning during gastrulation; however, the activities of these pathways in space and time have never been directly observed. In this study, we quantify BMP, WNT, and NODAL signaling dynamics in an in vitro model of human gastrulation. Our data suggest that BMP signaling initiates waves of WNT and NODAL signaling activity that move toward the colony center at a constant rate. Using a simple mathematical model, we show that this wave-like behavior is inconsistent with a reaction-diffusion-based Turing system, indicating that there is no stable signaling gradient of WNT/NODAL. Instead, the final signaling state is homogeneous, and spatial differences arise only from boundary effects. We further show that the durations of WNT and NODAL signaling control mesoderm differentiation, while the duration of BMP signaling controls differentiation of CDX2-positive extra-embryonic cells. The identity of these extra-embryonic cells has been controversial, and we use RNA sequencing (RNA-seq) to obtain their transcriptomes and show that they closely resemble human trophoblast cells in vivo. The domain of BMP signaling is identical to the domain of differentiation of these trophoblast-like cells; however, neither WNT nor NODAL forms a spatial pattern that maps directly to the mesodermal region, suggesting that mesoderm differentiation is controlled dynamically by the combinatorial effect of multiple signals. We synthesize our data into a mathematical model that accurately recapitulates signaling dynamics and predicts cell fate patterning upon chemical and physical perturbations. Taken together, our study shows that the dynamics of signaling events in the BMP, WNT, and NODAL cascade in the absence of a stable signaling gradient control fate patterning of human gastruloids.R01 GM126122 - NIGMS NIH HHSPublished versio

Spectral stability of pattern-forming fronts in the complex Ginzburg-Landau equation with a quenching mechanism

We consider pattern-forming fronts in the complex Ginzburg-Landau equation with a traveling spatial heterogeneity which destabilizes, or quenches, the trivial ground state while progressing through the domain. We consider the regime where the heterogeneity propagates with speed $c$ just below the linear invasion speed of the pattern-forming front in the associated homogeneous system. In this situation, the front locks to the interface of the heterogeneity leaving a long intermediate state lying near the unstable ground state, possibly allowing for growth of perturbations. This manifests itself in the spectrum of the linearization about the front through the accumulation of eigenvalues onto the absolute spectrum associated with the unstable ground state. As the quench speed $c$ increases towards the linear invasion speed, the absolute spectrum stabilizes with the same rate at which eigenvalues accumulate onto it allowing us to rigorously establish spectrally stability of the front in $L^2(\mathbb{R})$. The presence of unstable absolute spectrum poses a technical challenge as spatial eigenvalues along the intermediate state no longer admit a hyperbolic splitting and standard tools such as exponential dichotomies are unavailable. Instead, we projectivize the linear flow, and use Riemann surface unfolding in combination with a superposition principle to study the evolution of subspaces as solutions to the associated matrix Riccati differential equation on the Grassmannian manifold. Eigenvalues can then be identified as the roots of the meromorphic Riccati-Evans function, and can be located using winding number and parity arguments

Spectral stability of pattern-forming fronts in the complex Ginzburg-Landau equation with a quenching mechanism

We consider pattern-forming fronts in the complex Ginzburg-Landau equation with a traveling spatial heterogeneity which destabilizes, or quenches, the trivial ground state while progressing through the domain. We consider the regime where the heterogeneity propagates with speed $c$ just below the linear invasion speed of the pattern-forming front in the associated homogeneous system. In this situation, the front locks to the interface of the heterogeneity leaving a long intermediate state lying near the unstable ground state, possibly allowing for growth of perturbations. This manifests itself in the spectrum of the linearization about the front through the accumulation of eigenvalues onto the absolute spectrum associated with the unstable ground state. As the quench speed $c$ increases towards the linear invasion speed, the absolute spectrum stabilizes with the same rate at which eigenvalues accumulate onto it allowing us to rigorously establish spectrally stability of the front in $L^2(\mathbb{R})$. The presence of unstable absolute spectrum poses a technical challenge as spatial eigenvalues along the intermediate state no longer admit a hyperbolic splitting and standard tools such as exponential dichotomies are unavailable. Instead, we projectivize the linear flow, and use Riemann surface unfolding in combination with a superposition principle to study the evolution of subspaces as solutions to the associated matrix Riccati differential equation on the Grassmannian manifold. Eigenvalues can then be identified as the roots of the meromorphic Riccati-Evans function, and can be located using winding number and parity arguments

Smart and Sustainable Aquaponics

As the global population increases, new ways of sustainable and efficient food production need to be explored in order to meet the growing demand from society. In this paper we explore the methods and functionality of an off-grid, semi-autonomous aquaponics system. This system will serve as a proof of concept for a large scale aquaponics system which can be modelled in other parts of the world where arable land is scarce. It was found that though the initial startup costs are high, it will be able to reduce the cost of food in the long run. The system implements a solar array and battery system, lighting, temperature controls and a plumbing system

Pattern formation in the wake of external mechanisms

University of Minnesota Ph.D. dissertation. June 2016. Major: Mathematics. Advisor: Arnd Scheel. 1 computer file (PDF); xiii, 189 pages.Pattern formation in nature has intrigued humans for centuries, if not millennia. In the past few decades researchers have become interested in harnessing these processes to engineer and manufacture self-organized and self-regulated devices at various length scales. Since many natural pattern forming processes nucleate or grow from a homogeneous unstable state, they typically create defects, caused by thermal and other inherent sources of noise, which can hamper effectiveness in applications. One successful experimental method for controlling the pattern forming process is to use an external mechanism which moves through a system, transforming it from a stable state to an unstable state from which the pattern forming dynamics can take hold. In this thesis, we rigorously study partial differential equations which model how such triggering mechanisms can select and control patterns. We first use dynamical systems techniques to study the case where a spatial trigger perturbs a pattern forming freely invading front in a scalar partial differential equation. We study such perturbations for the two generic types of scalar invasion fronts, known as pulled and pushed fronts, which roughly correspond to fronts which invade either through a linear or nonlinear mechanism. Our results give the existence of perturbed fronts and provide expansions in the speed of the triggering mechanism for the wavenumber perturbation of the pattern formed. With the hope of moving towards the more complicated geometries which can arise in two spatial dimensions, where many dynamical systems methods cannot be readily applied, we also develop a functional analytic method for the study of Hopf bifurcation in the presence of continuous spectrum. Our method, while still giving computable information about the bifurcating solution, is more direct than previously proposed methods. We develop this method in the context of a triggered Cahn-Hilliard equation, in one spatial dimension, which has been used to study many triggered pattern forming systems. Furthermore, we use these abstract results to characterize an explicit example and also use our method to give a simplified proof of the bifurcation of oscillatory shock solutions in viscous conservation laws