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

Pattern formation for the Swift-Hohenberg equation on the hyperbolic plane

We present an overview of pattern formation analysis for an analogue of the Swift-Hohenberg equation posed on the real hyperbolic space of dimension two, which we identify with the Poincar\'e disc D. Different types of patterns are considered: spatially periodic stationary solutions, radial solutions and traveling waves, however there are significant differences in the results with the Euclidean case. We apply equivariant bifurcation theory to the study of spatially periodic solutions on a given lattice of D also called H-planforms in reference with the "planforms" introduced for pattern formation in Euclidean space. We consider in details the case of the regular octagonal lattice and give a complete descriptions of all H-planforms bifurcating in this case. For radial solutions (in geodesic polar coordinates), we present a result of existence for stationary localized radial solutions, which we have adapted from techniques on the Euclidean plane. Finally, we show that unlike the Euclidean case, the Swift-Hohenberg equation in the hyperbolic plane undergoes a Hopf bifurcation to traveling waves which are invariant along horocycles of D and periodic in the "transverse" direction. We highlight our theoretical results with a selection of numerical simulations.Comment: Dedicated to Klaus Kirchg\"assne

The thermodynamics for a hadronic gas of fireballs with internal color structures and chiral fields

The thermodynamical partition function for a gas of color-singlet bags consisting of fundamental and adjoint particles in both $U(N_c)$ and $SU(N_c)$ group representations is reviewed in detail. The constituent particle species are assumed to satisfy various thermodynamical statistics. The gas of bags is probed to study the phase transition for a nuclear matter in the extreme conditions. These bags are interpreted as the Hagedorn states and they are the highly excited hadronic states which are produced below the phase transition point to the quark-gluon plasma. The hadronic density of states has the Gross-Witten critical point and exhibits a third order phase transition from a hadronic phase dominated by the discrete low-lying hadronic mass spectrum particles to another hadronic phase dominated by the continuous Hagedorn states. The Hagedorn threshold production is found just above the highest known experimental discrete low-lying hadronic mass spectrum. The subsequent Hagedorn phase undergoes a first order deconfinement phase transition to an explosive quark-gluon plasma. The role of the chiral phase transition in the phases of the discrete low-lying mass spectrum and the continuous Hagedorn mass spectrum is also considered. It is found crucial in the phase transition diagram. Alternate scenarios are briefly discussed for the Hagedorn gas undergoes a higher order phase transition through multi-processes of internal color-flavor structure modification.Comment: 110 pages and 13 figures. Added references to the introductio

A High-Order Kernel Method for Diffusion and Reaction-Diffusion Equations on Surfaces

In this paper we present a high-order kernel method for numerically solving diffusion and reaction-diffusion partial differential equations (PDEs) on smooth, closed surfaces embedded in $\mathbb{R}^d$. For two-dimensional surfaces embedded in $\mathbb{R}^3$, these types of problems have received growing interest in biology, chemistry, and computer graphics to model such things as diffusion of chemicals on biological cells or membranes, pattern formations in biology, nonlinear chemical oscillators in excitable media, and texture mappings. Our kernel method is based on radial basis functions (RBFs) and uses a semi-discrete approach (or the method-of-lines) in which the surface derivative operators that appear in the PDEs are approximated using collocation. The method only requires nodes at "scattered" locations on the surface and the corresponding normal vectors to the surface. Additionally, it does not rely on any surface-based metrics and avoids any intrinsic coordinate systems, and thus does not suffer from any coordinate distortions or singularities. We provide error estimates for the kernel-based approximate surface derivative operators and numerically study the accuracy and stability of the method. Applications to different non-linear systems of PDEs that arise in biology and chemistry are also presented

Loop exponent in DNA bubble dynamics

Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting time and meeting position probability distributions are derived from the solutions. Probability distribution functions reflect the value of the loop exponent of the entropic interaction. Our results extend previous results which concentrated mainly on the tails of the probability distribution functions and open a way to determining the strength of the entropic interaction experimentally which has been a matter of recent discussions. Using numerical integration, we also discuss the influence of the finite size of a DNA chain on the bubble dynamics. Analogous results are obtained also for the case of subdiffusive dynamics of a DNA bubble in a heteropolymer, revealing highly universal asymptotics of meeting time and position probability functions.Comment: 24 pages, 11 figures, text identical to the published version; v3 - updated Ref. [47] and corrected Eqs. (3.6) and (3.10

A Multiscale Diffuse-Interface Model for Two-Phase Flow in Porous Media

In this paper we consider a multiscale phase-field model for capillarity-driven flows in porous media. The presented model constitutes a reduction of the conventional Navier-Stokes-Cahn-Hilliard phase-field model, valid in situations where interest is restricted to dynamical and equilibrium behavior in an aggregated sense, rather than a precise description of microscale flow phenomena. The model is based on averaging of the equation of motion, thereby yielding a significant reduction in the complexity of the underlying Navier-Stokes-Cahn-Hilliard equations, while retaining its macroscopic dynamical and equilibrium properties. Numerical results are presented for the representative 2-dimensional capillary-rise problem pertaining to two closely spaced vertical plates with both identical and disparate wetting properties. Comparison with analytical solutions for these test cases corroborates the accuracy of the presented multiscale model. In addition, we present results for a capillary-rise problem with a non-trivial geometry corresponding to a porous medium