Numerical bifurcation diagram for the two-dimensional boundary-fed chlorine-dioxide–iodine–malonic-acid system

We present a numerical solution of the chlorine-dioxide–iodine–malonic-acid reaction-diffusion system in two dimensions in a boundary-fed system using a realistic model. The bifurcation diagram for the transition from nonsymmetry-breaking structures along boundary feed gradients to transverse symmetry-breaking patterns in a single layer is numerically determined. We find this transition to be discontinuous. We make a connection with earlier results and discuss prospects for future work

Scroll Waves in the Presence of Slowly Varying Anisotropy with Application to the Heart

We consider the dynamics of scroll waves in the presence of rotating anisotropy, a model of the left ventricle of the heart in which the orientation of fibers in successive layers of tissue rotates. By choosing a coordinate system aligned with the fiber rotation and studying the phase dynamics of a straight but twisted scroll wave, we derive a Burgers’ equation with forcing associated with the fiber rotation rate. We present asymptotic solutions for scroll twist, verified by numerics, using a realistic fiber distribution profile. We make connection with earlier numerical and analytical work on scroll dynamics

The cytoplasm of living cells: A functional mixture of thousands of components

Inside every living cell is the cytoplasm: a fluid mixture of thousands of different macromolecules, predominantly proteins. This mixture is where most of the biochemistry occurs that enables living cells to function, and it is perhaps the most complex liquid on earth. Here we take an inventory of what is actually in this mixture. Recent genome-sequencing work has given us for the first time at least some information on all of these thousands of components. Having done so we consider two physical phenomena in the cytoplasm: diffusion and possible phase separation. Diffusion is slower in the highly crowded cytoplasm than in dilute solution. Reasonable estimates of this slowdown can be obtained and their consequences explored, for example, monomer-dimer equilibria are established approximately twenty times slower than in a dilute solution. Phase separation in all except exceptional cells appears not to be a problem, despite the high density and so strong protein-protein interactions present. We suggest that this may be partially a byproduct of the evolution of other properties, and partially a result of the huge number of components present.Comment: 11 pages, 1 figure, 1 tabl

Turing Instability in a Boundary-fed System

The formation of localized structures in the chlorine dioxide-idodine-malonic acid (CDIMA) reaction-diffusion system is investigated numerically using a realistic model of this system. We analyze the one-dimensional patterns formed along the gradients imposed by boundary feeds, and study their linear stability to symmetry-breaking perturbations (Turing instability) in the plane transverse to these gradients. We establish that an often-invoked simple local linear analysis which neglects longitudinal diffusion is inappropriate for predicting the linear stability of these patterns. Using a fully nonuniform analysis, we investigate the structure of the patterns formed along the gradients and their stability to transverse Turing pattern formation as a function of the values of two control parameters: the malonic acid feed concentration and the size of the reactor in the dimension along the gradients. The results from this investigation are compared with existing experiments.Comment: 41 pages, 18 figures, to be published in Physical Review

Scroll waves in isotropic excitable media : linear instabilities, bifurcations and restabilized states

Scroll waves are three-dimensional analogs of spiral waves. The linear stability spectrum of untwisted and twisted scroll waves is computed for a two-variable reaction-diffusion model of an excitable medium. Different bands of modes are seen to be unstable in different regions of parameter space. The corresponding bifurcations and bifurcated states are characterized by performing direct numerical simulations. In addition, computations of the adjoint linear stability operator eigenmodes are also performed and serve to obtain a number of matrix elements characterizing the long-wavelength deformations of scroll waves.Comment: 30 pages 16 figures, submitted to Phys. Rev.

Gravitational clustering of relic neutrinos and implications for their detection

We study the gravitational clustering of big bang relic neutrinos onto existing cold dark matter (CDM) and baryonic structures within the flat $\Lambda$CDM model, using both numerical simulations and a semi-analytical linear technique, with the aim of understanding the neutrinos' clustering properties for direct detection purposes. In a comparative analysis, we find that the linear technique systematically underestimates the amount of clustering for a wide range of CDM halo and neutrino masses. This invalidates earlier claims of the technique's applicability. We then compute the exact phase space distribution of relic neutrinos in our neighbourhood at Earth, and estimate the large scale neutrino density contrasts within the local Greisen--Zatsepin--Kuzmin zone. With these findings, we discuss the implications of gravitational neutrino clustering for scattering-based detection methods, ranging from flux detection via Cavendish-type torsion balances, to target detection using accelerator beams and cosmic rays. For emission spectroscopy via resonant annihilation of extremely energetic cosmic neutrinos on the relic neutrino background, we give new estimates for the expected enhancement in the event rates in the direction of the Virgo cluster.Comment: 38 pages, 8 embedded figures, iopart.cls; v2: references added, minor changes in text, to appear in JCA

Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations

We review the application of mathematical modeling to understanding the behavior of populations of chemotactic bacteria. The application of continuum mathematical models, in particular generalized Keller–Segel models, is discussed along with attempts to incorporate the microscale (individual) behavior on the macroscale, modeling the interaction between different species of bacteria, the interaction of bacteria with their environment, and methods used to obtain experimentally verified parameter values. We allude briefly to the role of modeling pattern formation in understanding collective behavior within bacterial populations. Various aspects of each model are discussed and areas for possible future research are postulated