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Contact defects are time-periodic patterns in one space dimension that resemble spatially homogeneous oscillations with a defect embedded in their core region. For theoretical and numerical purposes, it is important to understand whether these defects persist when the domain is truncated to large spatial intervals, supplemented by appropriate boundary conditions. The present work shows that truncated contact defects exist and are unique on sufficiently large spatial intervals. [ABSTRACT FROM AUTHOR]

We consider the existence and spectral stability of periodic multi-pulse solutions in Hamiltonian systems which are translation invariant and reversible, for which the fifth-order Korteweg-de Vries equation is a prototypical example. We use Lin's method to construct multi-pulses on a periodic domain, and in particular demonstrate a pitchfork bifurcation structure for periodic double pulses. We also use Lin's method to reduce the spectral problem for periodic multi-pulses to computing the determinant of a block matrix, which encodes both eigenvalues resulting from interactions between neighboring pulses and eigenvalues associated with the essential spectrum. We then use this matrix to compute the spectrum associated with periodic single and double pulses. Most notably, we prove that brief instability bubbles form when eigenvalues collide on the imaginary axis as the periodic domain size is altered. These analytical results are all in good agreement with numerical computations, and numerical timestepping experiments demonstrate that these instability bubbles correspond to oscillatory instabilities. [ABSTRACT FROM AUTHOR]

Planar wave trains are traveling wave solutions whose wave profiles are periodic in one spatial direction and constant in the transverse direction. In this paper, we investigate the stability of planar wave trains in reaction-diffusion systems. We establish nonlinear diffusive stability against perturbations that are bounded along a line in R 2 and decay exponentially in the distance from this line. Our analysis is the first to treat spatially nonlocalized perturbations that do not originate from a phase modulation. We also consider perturbations that are fully localized and establish nonlinear stability with better decay rates, suggesting a trade-off between spatial localization of perturbations and temporal decay rate. Our stability analysis utilizes pointwise estimates to exploit the spatial structure of the perturbations. The nonlocalization of perturbations prevents the use of damping estimates in the nonlinear iteration scheme; instead, we track the perturbed solution in two different coordinate systems. [ABSTRACT FROM AUTHOR]

Localized planar patterns in spatially extended bistable systems are known to exist along intricate bifurcation diagrams, which are commonly referred to as snaking curves. Their analysis is challenging as techniques such as spatial dynamics that have been used to explain snaking in one space dimension no longer work in the planar case. Here, we consider bistable systems posed on square lattices and provide an analytical explanation of snaking near the anti-continuum limit using Lyapunov–Schmidt reduction. We also establish stability results for localized patterns, discuss bifurcations to asymmetric states, and provide further numerical evidence that the shape of snaking curves changes drastically as the coefficient that reflects the strength of the spatial coupling crosses a finite threshold. [ABSTRACT FROM AUTHOR]

We investigate stationary, spatially localized patterns in lattice dynamical systems that exhibit bistability. The profiles associated with these patterns have a long plateau where the pattern resembles one of the bistable states, while the profile is close to the second bistable state outside this plateau. We show that the existence branches of such patterns generically form either an infinite stack of closed loops (isolas) or intertwined s-shaped curves (snaking). We then use bifurcation theory near the anti-continuum limit, where the coupling between edges in the lattice vanishes, to prove existence of isolas and snaking in a bistable discrete real Ginzburg–Landau equation. We also provide numerical evidence for the existence of snaking diagrams for planar localized patches on square and hexagonal lattices and outline a strategy to analyse them rigorously. [ABSTRACT FROM AUTHOR]

Spiral wave patterns observed in models of cardiac arrhythmias and chemical oscillations develop alternans and stationary line defects, which can both be thought of as period-doubling instabilities. These instabilities are observed on bounded domains and may be caused by the spiral core, far-field asymptotics, or boundary conditions. Here, we introduce a methodology to disentangle the impacts of each region on the instabilities by analyzing spectral properties of spiral waves and boundary sinks on bounded domains with appropriate boundary conditions. We apply our techniques to spirals formed in reaction-diffusion systems to investigate how and why alternans and line defects develop. Our results indicate that the mechanisms driving these instabilities are quite different; alternans are driven by the spiral core, whereas line defects appear from boundary effects. Moreover, we find that the shape of the alternans eigenfunction is due to the interaction of a point eigenvalue with curves of continuous spectra. [ABSTRACT FROM AUTHOR]

We consider Reaction-Diffusion systems on R , and prove diffusive mixing of asymptotic states u 0 (k x - ϕ ± , k) , where u0 is a spectrally stable periodic wave. Our analysis is the first to treat arbitrarily large phase-offsets ϕ d = ϕ + - ϕ - , so long as this offset proceeds in a sufficiently regular manner. The offset ϕ d completely determines the size of the asymptotic profiles in any topology, placing our analysis in the large data setting. In addition, the present result is a global stability result, in the sense that the class of initial data considered is not near the asymptotic profile in any sense. We prove the global existence, decay, and asymptotic self-similarity of the associated wavenumber equation. We develop a functional analytic framework to handle the linearized operator around large Burgers profiles via the exact integrability of the underlying Burgers flow. This framework enables us to prove a crucial, new mean-zero coercivity estimate, which we then combine with a nonlinear energy method. [ABSTRACT FROM AUTHOR]

Abstract Spatially localized patterns have been observed in numerous physical contexts, and their bifurcation diagrams often exhibit similar snaking behavior: symmetric solution branches, connected by bifurcating asymmetric solution branches, wind back and forth in an appropriate parameter. Previous papers have addressed existence of such solutions; here we address their stability, taking the necessary first step of unifying existence and uniqueness proofs for symmetric and asymmetric solutions. We then show that, under appropriate assumptions, temporal eigenvalues of the front and back underlying a localized solution are added with multiplicity in the right half plane. In a companion paper, we analyze the behavior of eigenvalues at λ = 0 and inside the essential spectrum. Our results show that localized snaking solutions are stable if, and only if, the underlying fronts and backs are stable: unlike localized non-oscillatory solutions, no interaction eigenvalues are present. We use the planar Swift–Hohenberg system to illustrate our results. [ABSTRACT FROM AUTHOR]

Planar wave trains are traveling wave solutions whose wave profiles are periodic in one spatial direction and constant in the transverse direction. In this paper, we investigate the stability of planar wave trains in reaction–diffusion systems. We establish nonlinear diffusive stability against perturbations that are bounded along a line in R 2 and decay exponentially in the distance from this line. Our analysis is the first to treat spatially nonlocalized perturbations that do not originate from a phase modulation. We also consider perturbations that are fully localized and establish nonlinear stability with better decay rates, suggesting a trade-off between spatial localization of perturbations and temporal decay rate. Our stability analysis utilizes pointwise estimates to exploit the spatial structure of the perturbations. The nonlocalization of perturbations prevents the use of damping estimates in the nonlinear iteration scheme; instead, we track the perturbed solution in two different coordinate systems. [ABSTRACT FROM AUTHOR]

The FitzHugh{Nagumo equations are known to admit fast traveling pulse solutions with monotone tails. It is also known that this system admits traveling pulses with exponentially decaying oscillatory tails. Upon numerical continuation in parameter space, it has been observed that the oscillations in the tails of the pulses grow into a secondary excursion resembling a second copy of the primary pulse. In this paper, we outline in detail the geometric mechanism responsible for this single-to-double-pulse transition, and we construct the transition analytically using geometric singular perturbation theory and blow-up techniques. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to give a short self-contained proof of the center-manifold theorem for maps and vector fields in finite-dimensional spaces using the graph transform. In particular, regularity of the center manifold is established using a direct argument that is based on the closedness of sets of differentiable functions whose highest derivatives are Lipschitz continuous in the space of continuous functions; this argument avoids the fiber contraction theorem that is commonly used in this context. [ABSTRACT FROM AUTHOR]

Numerical studies indicate that the FitzHugh-Nagumo system exhibits stable traveling pulses with oscillatory tails. In this paper, the existence of such pulses is proved analytically in the singular perturbation limit near parameter values where the FitzHugh-Nagumo system exhibits folds. In addition, the stability of these pulses is investigated numerically, and a mechanism is proposed that explains the transition from single to double pulses that was observed in earlier numerical studies. The existence proof utilizes geometric blow-up techniques combined with the exchange lemma: the main challenge is to understand the passage near two fold points on the slow manifold where normal hyperbolicity fails. [ABSTRACT FROM AUTHOR]

Abstract: In this article, we analyse bifurcations from stationary stable spots to travelling spots in a planar three-component FitzHugh–Nagumo system that was proposed previously as a phenomenological model of gas-discharge systems. By combining formal analyses, centre-manifold reductions, and detailed numerical continuation studies, we show that, in the parameter regime under consideration, the stationary spot destabilizes either through its zeroth Fourier mode in a Hopf bifurcation or through its first Fourier mode in a pitchfork or drift bifurcation, whilst the remaining Fourier modes appear to create only secondary bifurcations. Pitchfork bifurcations result in travelling spots, and we derive criteria for the criticality of these bifurcations. Our main finding is that supercritical drift bifurcations, leading to stable travelling spots, arise in this model, which does not seem possible for its two-component version. [Copyright &y& Elsevier]

Abstract: We expand upon a general framework for studying the bifurcation diagrams of localized spatially oscillatory structures. Building on work by Beck et al., the present work provides rigorous analytical results on the effects of perturbations to systems exhibiting snaking behavior. Starting with a reversible variational system possessing an additional symmetry, we elucidate the distinct effects of breaking symmetry and breaking variational structure, and characterize the resulting changes in both the bifurcation diagram and the solutions themselves. We show how to predict the branch reorganization and drift speeds induced by any particular given perturbative term, and illustrate our results via numerical continuation. We further demonstrate the utility of our methods in understanding the effects of particular perturbations breaking reversibility. Our approach yields an analytical explanation for previous numerical results on the effects of perturbations in the one-dimensional cubic–quintic Swift–Hohenberg model and allows us to make predictions on the effects of perturbations in more general settings, including planar systems. While our numerical results involve the Swift–Hohenberg model system, we emphasize the general applicability of the analytical results. [Copyright &y& Elsevier]

Reversible variational partial differential equations such as the Swift–Hohenberg equation can admit localized stationary roll structures whose solution branches are bounded in parameter space but unbounded in function space, with the width of the roll plateaus increasing without bound along the branch: this scenario is commonly referred to as snaking. In this work, the structure of the bifurcation diagrams of localized rolls is investigated for variational but non-reversible systems, and conditions are derived that guarantee snaking or result in diagrams that either consist entirely of isolas. [ABSTRACT FROM PUBLISHER]

Abstract: We consider reaction–diffusion systems on the infinite line that exhibit a family of spectrally stable spatially periodic wave trains that are parameterized by the wave number k. We prove stable diffusive mixing of the asymptotic states as with different phases at infinity for solutions that initially converge to these states as . The proof is based on Bloch wave analysis, renormalization theory, and a rigorous decomposition of the perturbations of these wave solutions into a phase mode, which shows diffusive behavior, and an exponentially damped remainder. Depending on the dispersion relation, the asymptotic states mix linearly with a Gaussian profile at lowest order or with a nonsymmetric non-Gaussian profile given by Burgers equation, which is the amplitude equation of the diffusive modes in the case of a nontrivial dispersion relation. [Copyright &y& Elsevier]

Localized planar patterns arise in many reaction-diffusion models. Most of the paradigm equations that have been studied so far are two-component models. While stationary localized structures are often found to be stable in such systems, travelling patterns either do not exist or are found to be unstable. In contrast, numerical simulations indicate that localized travelling structures can be stable in three-component systems. As a first step towards explaining this phenomenon, a planar singularly perturbed three-component reaction-diffusion system that arises in the context of gas-discharge systems is analysed in this paper. Using geometric singular perturbation theory, the existence and stability regions of radially symmetric stationary spot solutions are delineated and, in particular, stable spots are shown to exist in appropriate parameter regimes. This result opens up the possibility of identifying and analysing drift and Hopf bifurcations, and their criticality, from the stationary spots described here. [ABSTRACT FROM AUTHOR]

Abstract: The bifurcation structure of localized stationary radial patterns of the Swift–Hohenberg equation is explored when a continuous parameter is varied that corresponds to the underlying space dimension whenever is an integer. In particular, we investigate how 1D pulses and 2-pulses are connected to planar spots and rings when is increased from 1 to 2. We also elucidate changes in the snaking diagrams of spots when the dimension is switched from 2 to 3. [Copyright &y& Elsevier]

In order to understand the nonlinear stability of many types of time-periodic travelling waves on unbounded domains, one must overcome two main difficulties: the presence of embedded neutral eigenvalues and the time-dependence of the associated linear operator. This problem is studied in the context of time-periodic Lax shocks in systems of viscous conservation laws. Using spatial dynamics and a decomposition into separate Floquet eigenmodes, it is shown that the linear evolution for the time-dependent operator can be represented using a contour integral similar to that of the standard time-independent case. By decomposing the resulting Green’s distribution, the leading order behavior associated with the embedded eigenvalues is extracted. Sharp pointwise bounds are then obtained, which are used to prove that time-periodic Lax shocks are linearly and nonlinearly stable under the necessary conditions of spectral stability and minimal multiplicity of the translational eigenvalues. The latter conditions hold, for example, for small-oscillation time-periodic waves that emerge through a supercritical Hopf bifurcation from a family of time-independent Lax shocks of possibly large amplitude. [ABSTRACT FROM AUTHOR]

Abstract: Using Galerkin approximations, an Evans function for spatially periodic waves on infinite cylindrical domains is constructed. It is also shown that the Evans function can be used to define a parity index for periodic waves that detects whether the wave admits an odd number of real unstable eigenvalues. This parity index depends only on local information for the existence problem of the wave: in particular, it uses information about the linear dispersion relation near zero and the orientability of the unstable and stable manifolds along the nonlinear wave. The results are applied to small-amplitude wave trains for a scalar equation on an infinite strip. [Copyright &y& Elsevier]

Abstract: We investigate the existence and stability of standing and travelling multi-hump waves in partial differential equations with reflection and phase symmetries. We focus on 2- and 3-pulse solutions that arise near bi-foci and apply our results to the complex cubic-quintic Ginzburg–Landau equation. [Copyright &y& Elsevier]

We investigate stationary spatially localized hexagon patterns of the two-dimensional (2D) Swift- Hohenberg equation in the parameter region where the trivial state and regular hexagon patterns are both stable. Using numerical continuation techniques, we trace out the existence regions of fully localized hexagon patches and of planar pulses which consist of a strip filled with hexagons that is embedded in the trivial state. We find that these patterns exhibit snaking: for each parameter value in the snaking region, an infinite number of patterns exist that are connected in parameter space and whose width increases without bound. Our computations also indicate a relation between the limits of the snaking regions of planar hexagon pulses with different orientations and of the fully localized hexagon patches. To investigate which hexagons among the one-parameter family of hexagons are selected in a hexagon pulse or front, we derive a conserved quantity of the spatial dynamical system that describes planar patterns which are periodic in the transverse direction and use it to calculate the Maxwell curves along which the selected hexagons have the same energy as the trivial state. We find that the Maxwell curve lies within the snaking region, as expected from heuristic arguments. [ABSTRACT FROM AUTHOR]

Modeling networks of synaptically coupled neurons often leads to systems of integro-differential equations. Particularly interesting solutions in this context are traveling waves. We prove here that spectral stability of traveling waves implies their nonlinear stability in appropriate function spaces, and compare several recent Evans-function constructions that are useful tools when analyzing spectral stability. [ABSTRACT FROM AUTHOR]

Motivated by experimental observations in the light-sensitive Belousov—Zhabotinsky reaction and subsequent numerical works, we discuss period-doubling bifurcations of spiral waves and other coherent structures. We report on explanations of the observed phenomena which involve a detailed analysis of spectra, and of the associated eigenfunctions, of defects on bounded and unbounded domains. [ABSTRACT FROM AUTHOR]

Fronts are traveling waves in spatially extended systems that connect two different spatially homogeneous rest states. If the rest state behind the front undergoes a supercritical Turing instability, then the front will also destabilize. On the linear level, however, the front will be only convectively unstable since perturbations will be pushed away from the front as it propagates. In other words, perturbations may grow, but they can do so only behind the front. The goal of this paper is to prove for a specific model system that this behavior carries over to the full nonlinear system. [ABSTRACT FROM AUTHOR]

Abstract: A continuation approach to the computation of essential and absolute spectra of differential operators on the real line is presented. The advantages of this approach, compared with direct eigenvalue computations for the discretized operator, are the efficient and accurate computation of selected parts of the spectrum (typically those near the imaginary axis) and the option to compute nonlinear travelling waves and selected eigenvalues or other stability indicators simultaneously in order to locate accurately the onset to instability. We also discuss the implementation and usage of this approach with the software package auto and provide example computations for the FitzHugh–Nagumo and the complex Ginzburg–Landau equation. [Copyright &y& Elsevier]

Partial differential equations with time delays serve as models for systems where both spatial structure and memory effects are important. The asymptotic stability of travelling waves in such systems is still determined entirely by the spectrum of the linearization about the wave. We compare the spectra of localized waves on the unbounded real line with spectra computed on large intervals with appropriate boundary conditions applied at their end points. We show that the spectrum on large intervals approximates the spectrum on the real line when periodic boundary conditions are used. If separated boundary conditions are applied, it is the so-called absolute spectrum together with the extended point spectrum that is approximated; their union typically differs from the spectrum on the real line. [ABSTRACT FROM AUTHOR]

Using a scalar advection–reaction–diffusion equation with a cubic nonlinearity as a simple model problem, we investigate the effect of domain size on stability and bifurcations of steady states. We focus on two parameter regimes, namely, the regions where the steady state is convectively or absolutely unstable. In the convective–instability regime, the trivial stationary solution is asymptotically stable on any bounded domain but unstable on the real line. To measure the degree to which the trivial solution is stable, we estimate the distance of the trivial solution to the boundary of its basin of attraction: We show that this distance is exponentially small in the diameter of the domain for subcritical nonlinearities, while it is bounded away from zero uniformly in the domain size for supercritical nonlinearities. Lastly, at the onset of the absolute instability where the trivial steady state destabilizes on large bounded domains, we discuss bifurcations and amplitude scalings. [Copyright &y& Elsevier]

We investigate, in a systematic fashion, coherent structures, or defects, which serve as interfaces between wave trains with possibly different wavenumbers in reaction-diffusion systems. We propose a classification of defects into four different defect classes which have all been observed experimentally. The characteristic distinguishing these classes is the sign of the group velocities of the wave trains to either side of the defect, measured relative to the speed of the defect. Using a spatial-dynamics description in which defects correspond to homoclinic and heteroclinic connections of an ill-posed pseudoelliptic equation, we then relate robustness properties of defects to their spectral stability properties. Last , we illustrate that all four types of defects occur in the one-dimensional cubic- quintic Ginzburg-Landau equation as a perturbation of the phase-slip vortex. [ABSTRACT FROM AUTHOR]

In this article, existence and stability of N-front travelling-wave solutions of partial differential equations on the real line is investigated. The N-fronts considered here arise as heteroclinic orbits bifurcating from a twisted heteroclinic loop in the underlying ordinary differential equation describing travelling-wave solutions. It is proved that the N-front solutions are linearly stable provided the fronts building the twisted heteroclinic loop are linearly stable. The result is applied to travelling waves arising in the FitzHugh-Nagumo equation. [ABSTRACT FROM AUTHOR]

Recent advances in sequencing technologies have allowed us to capture various aspects of the genome at single-cell resolution. However, with the exception of a few of co-assaying technologies, it is not possible to simultaneously apply different sequencing assays on the same single cell. In this scenario, computational integration of multi-omic measurements is crucial to enable joint analyses. This integration task is particularly challenging due to the lack of sample-wise or feature-wise correspondences. We present single-cell alignment with optimal transport (SCOT), an unsupervised algorithm that uses the Gromov–Wasserstein optimal transport to align single-cell multi-omics data sets. SCOT performs on par with the current state-of-the-art unsupervised alignment methods, is faster, and requires tuning of fewer hyperparameters. More importantly, SCOT uses a self-tuning heuristic to guide hyperparameter selection based on the Gromov–Wasserstein distance. Thus, in the fully unsupervised setting, SCOT aligns single-cell data sets better than the existing methods without requiring any orthogonal correspondence information. [ABSTRACT FROM AUTHOR]

Although the availability of various sequencing technologies allows us to capture different genome properties at single-cell resolution, with the exception of a few co-assaying technologies, applying different sequencing assays on the same single cell is impossible. Single-cell alignment using optimal transport (SCOT) is an unsupervised algorithm that addresses this limitation by using optimal transport to align single-cell multiomics data. First, it preserves the local geometry by constructing a k-nearest neighbor (k-NN) graph for each data set (or domain) to capture the intra-domain distances. SCOT then finds a probabilistic coupling matrix that minimizes the discrepancy between the intra-domain distance matrices. Finally, it uses the coupling matrix to project one single-cell data set onto another through barycentric projection, thus aligning them. SCOT requires tuning only two hyperparameters and is robust to the choice of one. Furthermore, the Gromov-Wasserstein distance in the algorithm can guide SCOT's hyperparameter tuning in a fully unsupervised setting when no orthogonal alignment information is available. Thus, SCOT is a fast and accurate alignment method that provides a heuristic for hyperparameter selection in a real-world unsupervised single-cell data alignment scenario. We provide a tutorial for SCOT and make its source code publicly available on GitHub. [ABSTRACT FROM AUTHOR]

Identifying unique parameters for mathematical models describing biological data can be challenging and often impossible. Parameter identifiability for partial differential equations models in cell biology is especially difficult given that many established in vivo measurements of protein dynamics average out the spatial dimensions. Here, we are motivated by recent experiments on the binding dynamics of the RNA-binding protein PTBP3 in RNP granules of frog oocytes based on fluorescence recovery after photobleaching (FRAP) measurements. FRAP is a widely-used experimental technique for probing protein dynamics in living cells, and is often modeled using simple reaction-diffusion models of the protein dynamics. We show that current methods of structural and practical parameter identifiability provide limited insights into identifiability of kinetic parameters for these PDE models and spatially-averaged FRAP data. We thus propose a pipeline for assessing parameter identifiability and for learning parameter combinations based on re-parametrization and profile likelihoods analysis. We show that this method is able to recover parameter combinations for synthetic FRAP datasets and investigate its application to real experimental data. [ABSTRACT FROM AUTHOR]

Equation-free modeling aims at extracting low-dimensional macroscopic dynamics from complex high-dimensional systems that govern the evolution of microscopic states. This algorithm relies on lifting and restriction operators that map macroscopic states to microscopic states and vice versa. Combined with simulations of the microscopic state, this algorithm can be used to apply Newton solvers to the implicitly defined low-dimensional macroscopic system or solve it more efficiently using direct numerical simulations. The key challenge is the construction of the lifting and restrictions operators that usually require a priori insight into the underlying application. In this paper, we design an application-independent algorithm that uses diffusion maps to construct these operators from simulation data. Code is available at https://doi.org/10.5281/zenodo.5793299. [ABSTRACT FROM AUTHOR]

We study the structure of stationary patterns in bistable lattice dynamical systems posed on rings with a symmetric coupling structure in the regime of small coupling strength. We show that sparse coupling (for instance, nearest-neighbour or next-nearest-neighbour coupling) and all-to-all coupling lead to significantly different solution branches. In particular, sparse coupling leads to snaking branches with many saddle-node bifurcations, while all-to-all coupling leads to branches with six saddle nodes, regardless of the size of the number of nodes in the graph. [ABSTRACT FROM AUTHOR]

Motivated by pulse-replication phenomena observed in the FitzHugh--Nagumo equation, we investigate traveling pulses whose slow/fast profiles exhibit canard-like transitions. We show that the spectra of the PDE linearization about such pulses may contain many point eigenvalues that accumulate onto a union of curves as the slow scale parameter approaches zero. The limit sets are related to the absolute spectrum of the homogeneous rest states involved in the canard-like transitions. Our results are formulated for general systems that admit an appropriate slow/fast structure. [ABSTRACT FROM AUTHOR]

In its original formulation the Krein matrix was used to locate the spectrum of first-order star-even polynomial operators where both operator coefficients are nonsingular. Such operators naturally arise when considering first-order-in-time Hamiltonian PDEs. Herein the matrix is reformulated to allow for operator coefficients with nontrivi al kernel. Moreover, it is extended to allow for the study of the spectral problem associated with quadratic star-even operators, which arise when considering the spectral problem associated with second-order-in-time Hamiltonian PDEs. In conjunction with the Hamiltonian-Krein index (HKI) the Krein matrix is used to study two problems: conditions leading to Hamiltonian-Hopf bifurcations for small spatially periodic waves, and the location and Krein signature of small eigenvalues associated with, e.g., n-pulse problems. For the first case we consider in detail a first-order-in-time fifth-order KdV-like equation. In the latter case we use a combination of Lin's method, the HKI, and the Krein matrix to study the spectrum associated with n-pulses for a second-order-in-time Hamiltonian system which is used to model the dynamics of a suspension bridge. [ABSTRACT FROM AUTHOR]

Emerging large-scale biobanks pairing genotype data with phenotype data present new opportunities to prioritize shared genetic associations across multiple phenotypes for molecular validation. Past research, by our group and others, has shown gene-level tests of association produce biologically interpretable characterization of the genetic architecture of a given phenotype. Here, we present a new method, Ward clustering to identify Internal Node branch length outliers using Gene Scores (WINGS), for identifying shared genetic architecture among multiple phenotypes. The objective of WINGS is to identify groups of phenotypes, or "clusters," sharing a core set of genes enriched for mutations in cases. We validate WINGS using extensive simulation studies and then combine gene-level association tests with WINGS to identify shared genetic architecture among 81 case-control and seven quantitative phenotypes in 349,468 European-ancestry individuals from the UK Biobank. We identify eight prioritized phenotype clusters and recover multiple published gene-level associations within prioritized clusters. [ABSTRACT FROM AUTHOR]

Self-organized pattern behavior is ubiquitous throughout nature, from fish schooling to collective cell dynamics during organism development. Qualitatively these patterns display impressive consistency, yet variability inevitably exists within pattern-forming systems on both microscopic and macroscopic scales. Quantifying variability and measuring pattern features can inform the underlying agent interactions and allow for predictive analyses. Nevertheless, current methods for analyzing patterns that arise from collective behavior capture only macroscopic features or rely on either manual inspection or smoothing algorithms that lose the underlying agent-based nature of the data. Here we introduce methods based on topological data analysis and interpretable machine learning for quantifying both agent-level features and global pattern attributes on a large scale. Because the zebrafish is a model organism for skin pattern formation, we focus specifically on analyzing its skin patterns as a means of illustrating our approach. Using a recent agent-based model, we simulate thousands of wild-type and mutant zebrafish patterns and apply our methodology to better understand pattern variability in zebrafish. Our methodology is able to quantify the differential impact of stochasticity in cell interactions on wild-type and mutant patterns, and we use our methods to predict stripe and spot statistics as a function of varying cellular communication. Our work provides an approach to automatically quantifying biological patterns and analyzing agent-based dynamics so that we can now answer critical questions in pattern formation at a much larger scale. [ABSTRACT FROM AUTHOR]

Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other cell types. However, automated and unsupervised classification of these multicellular spatial patterns remains challenging, particularly given their structural diversity and biological variability. Recent developments based on topological data analysis are intriguing to reveal similarities in tissue architecture, but these methods remain computationally expensive. In this article, we show that multicellular patterns organized from two interacting cell types can be efficiently represented through persistence images. Our optimized combination of dimensionality reduction via autoencoders, combined with hierarchical clustering, achieved high classification accuracy for simulations with constant cell numbers. We further demonstrate that persistence images can be normalized to improve classification for simulations with varying cell numbers due to proliferation. Finally, we systematically consider the importance of incorporating different topological features as well as information about each cell type to improve classification accuracy. We envision that topological machine learning based on persistence images will enable versatile and robust classification of complex tissue architectures that occur in development and disease. [ABSTRACT FROM AUTHOR]

The Evans function has been used extensively to study spectral stability of travelling-wave solutions in spatially extended partial differential equations. To compute Evans functions numerically, several shooting methods have been developed. In this paper, an alternative scheme for the numerical computation of Evans functions is presented that relies on an appropriate boundary-value problem formulation. Convergence of the algorithm is proved, and several examples, including the computation of eigenvalues for a multi-dimensional problem, are given. The main advantage of the scheme proposed here compared with earlier methods is that the scheme is linear and scalable to large problems. [ABSTRACT FROM AUTHOR]

The FitzHugh-Nagumo equations are known to admit fast traveling pulses that have monotone tails and arise as the concatenation of Nagumo fronts and backs in an appropriate singular limit, where a parameter $$\varepsilon $$ goes to zero. These pulses are known to be nonlinearly stable with respect to the underlying PDE. Recently, the existence of fast pulses with oscillatory tails was proved for the FitzHugh-Nagumo equations. In this paper, we prove that the fast pulses with oscillatory tails are also nonlinearly stable. Similar to the case of monotone tails, stability is decided by the location of a nontrivial eigenvalue near the origin of the PDE linearization about the traveling pulse. We prove that this real eigenvalue is always negative. However, the expression that governs the sign of this eigenvalue for oscillatory pulses differs from that for monotone pulses, and we show indeed that the nontrivial eigenvalue in the monotone case scales with $$\varepsilon $$ , while the relevant scaling in the oscillatory case is $$\varepsilon ^{2/3}$$ . [ABSTRACT FROM AUTHOR]

In an appropriate moving coordinate frame, source defects are time-periodic solutions to reaction–diffusion equations that are spatially asymptotic to spatially periodic wave trains whose group velocities point away from the core of the defect. In this paper, we rigorously establish nonlinear stability of spectrally stable source defects in the complex Ginzburg–Landau equation. Due to the outward transport at the far field, localized perturbations may lead to a highly non-localized response even on the linear level. To overcome this, we first investigate in detail the dynamics of the solution to the linearized equation. This allows us to determine an approximate solution that satisfies the full equation up to and including quadratic terms in the nonlinearity. This approximation utilizes the fact that the non-localized phase response, resulting from the embedded zero eigenvalues, can be captured, to leading order, by the nonlinear Burgers equation. The analysis is completed by obtaining detailed estimates for the resolvent kernel and pointwise estimates for Green's function, which allow one to close a nonlinear iteration scheme. [ABSTRACT FROM AUTHOR]

Abstract: Coherent structures are solutions to reaction–diffusion systems that are time-periodic in an appropriate moving frame and spatially asymptotic at to spatially periodic travelling waves. This paper is concerned with sources which are coherent structures for which the group velocities in the far field point away from the core. Sources actively select wave numbers and therefore often organize the overall dynamics in a spatially extended system. Determining their nonlinear stability properties is challenging as localized perturbations may lead to a non-localized response even on the linear level due to the outward transport. Using a Burgers-type equation as a model problem that captures some of the essential features of sources, we show how this phenomenon can be analysed and asymptotic nonlinear stability be established in this simpler context. [Copyright &y& Elsevier]

Abstract: Operators on unbounded domains may acquire eigenvalues that are embedded in the essential spectrum. Determining the fate of these embedded eigenvalues under small perturbations of the underlying operator is a challenging task, and the persistence properties of such eigenvalues are linked intimately to the multiplicity of the essential spectrum. In this paper, we consider the planar bilaplacian with potential and show that the set of potentials for which an embedded eigenvalue persists is locally an infinite-dimensional manifold with infinite codimension in an appropriate space of potentials. [ABSTRACT FROM AUTHOR]

The nonlinear stability of traveling Lax shocks in semidiscrete conservation laws involving general spatial forward-backward discretization schemes is considered. It is shown that spectrally stable semidiscrete Lax shocks are nonlinearly stable. In addition, it is proved that weak semidiscrete Lax profiles satisfy the spectral stability hypotheses made here and are therefore non-linearly stable. The nonlinear stability results are proved by constructing the resolvent kernel using exponential dichotomies, which have recently been developed in this setting, and then using the contour integral representation for the associated Green's function to derive pointwise bounds that are su?cient for proving nonlinear stability. Previous stability analyses for semidiscrete shocks relied primarily on Evans functions, which exist only for one-sided upwind schemes. [ABSTRACT FROM AUTHOR]

Abstract: Reaction–diffusion equations on the real line that contain a control parameter are investigated. Of interest are travelling front solutions for which the rest state behind the front undergoes a supercritical Turing or Hopf bifurcation as the parameter is increased. This causes the essential spectrum to cross into the right half plane, leading to a linear convective instability in which the emerging pattern is pushed away from the front as it propagates. It is shown, however, that the wave remains nonlinearly stable in an appropriate sense. More precisely, using the fact that the instability is supercritical, it is shown that the amplitude of any pattern that emerges behind the wave saturates at some small parameter-dependent level and that the pattern is pushed away from the front interface. As a result, when considered in an appropriate exponentially weighted space, the travelling front remains stable, with an exponential in time rate of convergence. [Copyright &y& Elsevier]

Spectra of nonlinear waves in infinite-dimensional Hamiltonian systems are investigated. We establish a connection via the Krein signature between the number of negative directions of the second variation of the energy and the number of potentially unstable eigenvalues of the linearization about a nonlinear wave. We apply our results to determine the effect of symmetry breaking on the spectral stability of nonlinear waves in weakly coupled nonlinear Schrödinger equations. [Copyright &y& Elsevier]

Examines the dynamics of mode-locked lasers using Jacobi elliptic functions. Derivation of pulse-train solutions; Process of femtosecond modelocking in solid-state lasers; Occurrence of amplification in the cavity.