A mean-field model of superconducting vortices in three dimensions

A mean-field model for the motion of vortices in a type II superconductor is formulated, drawing on analogies with vortices in an inviscid fluid. The model admits discontinuous solutions, and the conditions on such an interface are derived. In a natural limiting case the model is shown to reduce to a novel, vectorial nonlinear diffusion equation. Finally, generalizations of the model to incorporate vortex pinning and fluctuation effects are described

A hierarchy of models for type-II superconductors

A hierarchy of models for type-II superconductors is presented. Through appropriate asymptotic limits we pass from the mesoscopic Ginzburg-Landau model to the London model with isolated superconducting vortices as line singularities, to vortex-density models, and finally to macroscopic critical-state models

Derivation of the bidomain equations for a beating heart with a general microstructure

A novel multiple scales method is formulated that can be applied to problems which have an almost\ud periodic microstructure not in Cartesian coordinates but in a general curvilinear coordinate system.\ud The method is applied to a model of the electrical activity of cardiac myocytes and used to derive a\ud version of the bidomain equations describing the macroscopic electrical activity of cardiac tissue. The\ud treatment systematically accounts for the non-uniform orientation of the cells within the tissue and for\ud deformations of the tissue occurring as a result of the heart beat

Exponential asymptotics and gravity waves

The problem of irrotational inviscid incompressible free-surface flow is examined in the limit of small Froude number. Since this is a singular perturbation, singularities in the flow field (or its analytic continuation) such as stagnation points, or corners in submerged objects or on rough beds, lead to a divergent asymptotic expansion, with associated Stokes lines. Recent techniques in exponential asymptotics are employed to observe the switching on of exponentially small gravity waves across these Stokes lines. As a concrete example, the flow over a step is considered. It is found that there are three possible parameter regimes, depending on whether the dimensionless step height is small, of the same order, or large compared to the square of the Froude number. Asymptotic results are derived in each case, and compared with numerical simulations of the full nonlinear problem. The agreement is remarkably good, even at relatively large Froude number. This is in contrast to the alternative analytical theory of small step height, which is accurate only for very small steps

Asymptotic approximation of eigenvalues of vector equations

A vectorial extension of the Keller-Rubinow method of computing asymptotic approximations of eigenvalues in bounded domains is presented. The method is applied to the problem of a multimode step-profile cylindrical optical fibre, including the effects of polarisation. A comparison of the asymptotic results with the exact eigenvalues is made when these are available, and the agreement is shown to be good

Stochastic modelling of reaction-diffusion processes:\ud algorithms for bimolecular reactions

Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice model described by the reaction-diffusion master equation. The second SSA is an off-lattice model based on the simulation of Brownian motion of individual molecules and their reactive collisions. In both cases, it is shown that the commonly used implementation of bimolecular reactions (i.e. the reactions of the form A+B → C, or A+A → C) might lead to incorrect results. Improvements of both SSAs are suggested which overcome the difficulties highlighted. In particular, a formula is presented for the smallest possible compartment size (lattice spacing) which can be correctly implemented in the first model. This implementation uses a new formula for the rate of bimolecular reactions per compartment (lattice site)

Exponentially slow transitions on a Markov chain: the frequency of Calcium Sparks

Calcium sparks in cardiac muscle cells occur when a cluster of Ca2+ channels open and release Ca2+ from an internal store. A simplified model of Ca2+ sparks has been developed to describe the dynamics of a cluster of channels, which is of the form of a continuous time Markov chain with nearest neighbour transitions and slowly varying jump functions. The chain displays metastability, whereby the probability distribution of the state of the system evolves exponentially slowly, with one of the metastable states occurring at the boundary. An asymptotic technique for analysing the Master equation (a differential-difference equation) associated with these Markov chains is developed using the WKB and projection methods. The method is used to re-derive a known result for a standard class of Markov chains displaying metastability, before being applied to the new class of Markov chains associated with the spark model. The mean first passage time between metastable states is calculated and an expression for the frequency of calcium sparks is derived. All asymptotic results are compared with Monte Carlo simulations

Time scale of random sequential adsorption

A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) the kinetics of the chemical reaction between adsorbing molecules and the surface; and (ii) geometrical constraints on the surface made by molecules which are already adsorbed. The process (i) is modelled in a diffusion-driven context, i.e. the conditional probability of adsorbing a molecule provided that the molecule hits the surface is related to the macroscopic surface reaction rate. The geometrical constraint (ii) is modelled using random sequential adsorption (RSA), which is the sequential addition of molecules at random positions on a surface; one attempt to attach a molecule is made per one RSA simulation time step. By coupling RSA with the diffusion of molecules in the solution above the surface the RSA simulation time step is related to the real physical time. The method is illustrated on a model of chemisorption of reactive polymers to a virus surface

Diffusion of finite-size particles in confined geometries

The diffusion of finite-size hard-core interacting particles in two- or three-dimensional confined domains is considered in the limit that the confinement dimensions become comparable to the particle’s dimensions. The result is a nonlinear diffusion equation for the one-particle probability density function, with an overall collective diffusion that depends on both the excluded-volume and the narrow confinement. By including both these effects the equation is able to interpolate between severe confinement (for example, single-file diffusion) and unconfined diffusion. Numerical solutions of both the effective nonlinear diffusion equation and the stochastic particle system are presented and compared. As an application, the case of diffusion under a ratchet potential is considered, and the change in transport properties due to excluded-volume and confinement effects is examined

A hierarchy of models for superconducting thin films

A hierarchy of models for type-II superconducting thin films is presented. Through appropriate asymptotic limits this hierarchy passes from the mesoscopic Ginzburg--Landau model to the London model with isolated vortices as $\delta$-function singularities to vortex-density models and finally to macroscopic critical-state models. At each stage it is found that a key nondimensional parameter is $\Lambda = \lambda^2/d L$, where $\lambda$ is the penetration depth of the magnetic field, a material parameter, and d and L are a typical thickness and lateral dimension of the film,respectively. The models simplify greatly if this parameter is large or small