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Circle maps frequently arise in mathematical models of physical or biological systems. Motivated by Cherry flows and `threshold' systems such as integrate and fire neuronal models, models of cardiac arrhythmias, and models of sleep/wake regulation, we consider how structural transitions in circle maps occur. In particular we describe how maps evolve near the creation of a discontinuity. We show that the natural way to create discontinuities in the maps associated with both threshold systems and Cherry flows results in a square root singularity in the map as the discontinuity is approached from either one or both sides. We analyse the generic properties of maps with gaps displaying this local behaviour, showing how border collisions and saddle-node bifurcations are interspersed. This highlights how the Arnold tongue picture for tongues bordered by saddle-node bifurcations is amended once gaps are present. For the threshold models we also show that a loss of injectivity naturally results in the creation of multiple gaps giving rise to a novel codimension two bifurcation., Comment: 33 pages, 13 figures

The Human Cell Atlas (HCA) will be made up of comprehensive reference maps of all human cells - the fundamental units of life - as a basis for understanding fundamental human biological processes and diagnosing, monitoring, and treating disease. It will help scientists understand how genetic variants impact disease risk, define drug toxicities, discover better therapies, and advance regenerative medicine. A resource of such ambition and scale should be built in stages, increasing in size, breadth, and resolution as technologies develop and understanding deepens. We will therefore pursue Phase 1 as a suite of flagship projects in key tissues, systems, and organs. We will bring together experts in biology, medicine, genomics, technology development and computation (including data analysis, software engineering, and visualization). We will also need standardized experimental and computational methods that will allow us to compare diverse cell and tissue types - and samples across human communities - in consistent ways, ensuring that the resulting resource is truly global. This document, the first version of the HCA White Paper, was written by experts in the field with feedback and suggestions from the HCA community, gathered during recent international meetings. The White Paper, released at the close of this yearlong planning process, will be a living document that evolves as the HCA community provides additional feedback, as technological and computational advances are made, and as lessons are learned during the construction of the atlas.

The Faraday problem is an important pattern-forming system that provides some middle ground between systems where the initial instability involves just a single mode and in which complexity then results from mode interactions or secondary bifurcations, and cases where a system is highly turbulent and many spatial and temporal modes are excited. It has been a rich source of novel patterns and of theoretical work aimed at understanding how and why such patterns occur. Yet it is particularly challenging to tie theory to experiment: the experiments are difficult to perform; the parameter regime of interest (large box, moderate viscosity) along with the technical difficulties of solving the free boundary Navier--Stokes equations make numerical solution of the problem hard; and the fact that the instabilities result in an entire circle of unstable wavevectors presents considerable theoretical difficulties. In principle, weakly nonlinear theory should be able to predict which patterns are stable near pattern onset. In this paper we present the first quantitative comparison between weakly nonlinear theory of the full Navier-Stokes equations and (previously published) experimental results for the Faraday problem with multiple frequency forcing. We confirm that three-wave interactions sit at the heart of why complex patterns are stablised but also highlight some discrepancies between theory and experiment. These suggest the need for further experimental and theoretical work to fully investigate the issues of pattern bistability and the role of bicritical/tricritical points in determining bifurcation structure., Comment: 30 pages, 15 figures

Sleep is essential for the maintenance of the brain and the body, yet many features of sleep are poorly understood and mathematical models are an important tool for probing proposed biological mechanisms. The most well-known mathematical model of sleep regulation, the two-process model, models the sleep-wake cycle by two oscillators: a circadian oscillator and a homeostatic oscillator. An alternative, more recent, model considers the mutual inhibition of sleep promoting neurons and the ascending arousal system regulated by homeostatic and circadian processes. Here we show there are fundamental similarities between these two models. The implications are illustrated with two important sleep-wake phenomena. Firstly, we show that in the two-process model, transitions between different numbers of daily sleep episodes occur at grazing bifurcations.This provides the theoretical underpinning for numerical results showing that the sleep patterns of many mammals can be explained by the mutual inhibition model. Secondly, we show that when sleep deprivation disrupts the sleep-wake cycle, ostensibly different measures of sleepiness in the two models are closely related. The demonstration of the mathematical similarities of the two models is valuable because not only does it allow some features of the two-process model to be interpreted physiologically but it also means that knowledge gained from study of the two-process model can be used to inform understanding of the mutual inhibition model. This is important because the mutual inhibition model and its extensions are increasingly being used as a tool to understand a diverse range of sleep-wake phenomena such as the design of optimal shift-patterns, yet the values it uses for parameters associated with the circadian and homeostatic processes are very different from those that have been experimentally measured in the context of the two-process model.

Three-wave interactions form the basis of our understanding of many pattern forming systems because they encapsulate the most basic nonlinear interactions. In problems with two comparable length scales, it is possible for two waves of the shorter wavelength to interact with one wave of the longer, as well as for two waves of the longer wavelength to interact with one wave of the shorter. Consideration of both types of three-wave interactions can generically explain the presence of complex patterns and spatio-temporal chaos. Two length scales arise naturally in the Faraday wave experiment with multi-frequency forcing, and our results enable some previously unexplained experimental observations of spatio-temporal chaos to be interpreted in a new light. Our predictions are illustrated with numerical simulations of a model partial differential equation., Comment: 4 pages, 3 figures, revised version

Dual recycling is an advanced optical technique to enhance the signal-to-noise ratio of laser interferometric gravitational wave detectors in a limited bandwidth. To optimise the center of this band with respect to Fourier frequencies of expected gravitational wave signals detuned dual recycling has to be implemented. We demonstrated detuned dual recycling on a fully suspended 30m prototype interferometer. A control scheme that allows to tune the detector to different frequencies will be outlined. Good agreement between the experimental results and numerical simulations has been achieved., Comment: 9 pages

Recent experiments (Kudrolli, Pier and Gollub, 1998) on two-frequency parametrically excited surface waves exhibit an intriguing "superlattice" wave pattern near a codimension-two bifurcation point where both subharmonic and harmonic waves onset simultaneously, but with different spatial wavenumbers. The superlattice pattern is synchronous with the forcing, spatially periodic on a large hexagonal lattice, and exhibits small-scale triangular structure. Similar patterns have been shown to exist as primary solution branches of a generic 12-dimensional $D_6\dot{+}T^2$-equivariant bifurcation problem, and may be stable if the nonlinear coefficients of the bifurcation problem satisfy certain inequalities (Silber and Proctor, 1998). Here we use the spatial and temporal symmetries of the problem to argue that weakly damped harmonic waves may be critical to understanding the stabilization of this pattern in the Faraday system. We illustrate this mechanism by considering the equations developed by Zhang and Vinals (1997, J. Fluid Mech. 336) for small amplitude, weakly damped surface waves on a semi-infinite fluid layer. We compute the relevant nonlinear coefficients in the bifurcation equations describing the onset of patterns for excitation frequency ratios of 2/3 and 6/7. For the 2/3 case, we show that there is a fundamental difference in the pattern selection problems for subharmonic and harmonic instabilities near the codimension-two point. Also, we find that the 6/7 case is significantly different from the 2/3 case due to the presence of additional weakly damped harmonic modes. These additional harmonic modes can result in a stabilization of the superpatterns., Comment: 26 pages, 8 figures; minor text revisions, corrected figure 8; this version to appear in a special issue of Physica D in memory of John David Crawford

Motivated by experimental observations of exotic standing wave patterns in the two-frequency Faraday experiment, we investigate the role of normal form symmetries in the pattern selection problem. With forcing frequency components in ratio m/n, where m and n are co-prime integers, there is the possibility that both harmonic and subharmonic waves may lose stability simultaneously, each with a different wavenumber. We focus on this situation and compare the case where the harmonic waves have a longer wavelength than the subharmonic waves with the case where the harmonic waves have a shorter wavelength. We show that in the former case a normal form transformation can be used to remove all quadratic terms from the amplitude equations governing the relevant resonant triad interactions. Thus the role of resonant triads in the pattern selection problem is greatly diminished in this situation. We verify our general results within the example of one-dimensional surface wave solutions of the Zhang-Vinals model of the two-frequency Faraday problem. In one-dimension, a 1:2 spatial resonance takes the place of a resonant triad in our investigation. We find that when the bifurcating modes are in this spatial resonance, it dramatically effects the bifurcation to subharmonic waves in the case of forcing frequencies are in ratio 1/2; this is consistent with the results of Zhang and Vinals. In sharp contrast, we find that when the forcing frequencies are in ratio 2/3, the bifurcation to (sub)harmonic waves is insensitive to the presence of another spatially-resonant bifurcating mode., Comment: 22 pages, 6 figures, latex

We consider the transition from a spatially uniform state to a steady, spatially-periodic pattern in a partial differential equation describing long-wavelength convection. This both extends existing work on the study of rolls, squares and hexagons and demonstrates how recent generic results for the stability of spatially-periodic patterns may be applied in practice. We find that squares, even if stable to roll perturbations, are often unstable when a wider class of perturbations is considered. We also find scenarios where transitions from hexagons to rectangles can occur. In some cases we find that, near onset, more exotic spatially-periodic planforms are preferred over the usual rolls, squares and hexagons., Comment: 25 pages, 8 figures

We consider the symmetry-breaking steady state bifurcation of a spatially-uniform equilibrium solution of E(2)-equivariant PDEs. We restrict the space of solutions to those that are doubly-periodic with respect to a square or hexagonal lattice, and consider the bifurcation problem restricted to a finite-dimensional center manifold. For the square lattice we assume that the kernel of the linear operator, at the bifurcation point, consists of 4 complex Fourier modes, with wave vectors K_1=(a,b), K_2=(-b,a), K_3=(b,a), and K_4=(-a,b), where a>b>0 are integers. For the hexagonal lattice, we assume that the kernel of the linear operator consists of 6 complex Fourier modes, also parameterized by an integer pair (a,b). We derive normal forms for the bifurcation problems, which we use to compute the linear, orbital stability of those solution branches guaranteed to exist by the equivariant branching lemma. These solutions consist of rolls, squares, hexagons, a countable set of rhombs, and a countable set of planforms that are superpositions of all of the Fourier modes in the kernel. Since rolls and squares (hexagons) are common to all of the bifurcation problems posed on square (hexagonal) lattices, this framework can be used to determine their stability relative to a countable set of perturbations by varying a and b. For the hexagonal lattice, we analyze the degenerate bifurcation problem obtained by setting the coefficient of the quadratic term to zero. The unfolding of the degenerate bifurcation problem reveals a new class of secondary bifurcations on the hexagons and rhombs solution branches., Comment: 62 pages (with figures), uuencoded, compressed postscript file