Status of the differential transformation method

Further to a recent controversy on whether the differential transformation method (DTM) for solving a differential equation is purely and solely the traditional Taylor series method, it is emphasized that the DTM is currently used, often only, as a technique for (analytically) calculating the power series of the solution (in terms of the initial value parameters). Sometimes, a piecewise analytic continuation process is implemented either in a numerical routine (e.g., within a shooting method) or in a semi-analytical procedure (e.g., to solve a boundary value problem). Emphasized also is the fact that, at the time of its invention, the currently-used basic ingredients of the DTM (that transform a differential equation into a difference equation of same order that is iteratively solvable) were already known for a long time by the "traditional"-Taylor-method users (notably in the elaboration of software packages --numerical routines-- for automatically solving ordinary differential equations). At now, the defenders of the DTM still ignore the, though much better developed, studies of the "traditional"-Taylor-method users who, in turn, seem to ignore similarly the existence of the DTM. The DTM has been given an apparent strong formalization (set on the same footing as the Fourier, Laplace or Mellin transformations). Though often used trivially, it is easily attainable and easily adaptable to different kinds of differentiation procedures. That has made it very attractive. Hence applications to various problems of the Taylor method, and more generally of the power series method (including noninteger powers) has been sketched. It seems that its potential has not been exploited as it could be. After a discussion on the reasons of the "misunderstandings" which have caused the controversy, the preceding topics are concretely illustrated.Comment: To appear in Applied Mathematics and Computation, 29 pages, references and further considerations adde

Odeint - Solving ordinary differential equations in C++

Many physical, biological or chemical systems are modeled by ordinary differential equations (ODEs) and finding their solution is an every-day-task for many scientists. Here, we introduce a new C++ library dedicated to find numerical solutions of initial value problems of ODEs: odeint (www.odeint.com). odeint is implemented in a highly generic way and provides extensive interoperability at top performance. For example, due to it's modular design it can be easily parallized with OpenMP and even runs on CUDA GPUs. Despite that, it provides a convenient interface that allows for a simple and easy usage.Comment: 4 pages, 1 figur

Rush-Larsen time-stepping methods of high order for stiff problems in cardiac electrophysiology

To address the issues of stability and accuracy for reaction-diffusion equations, the development of high order and stable time-stepping methods is necessary. This is particularly true in the context of cardiac electrophysiology, where reaction-diffusion equations are coupled with stiff ODE systems. Many research have been led in that way in the past 15 years concerning implicit-explicit methods and exponential integrators. In 2009, Perego and Veneziani proposed an innovative time-stepping method of order 2. In this paper we present the extension of this method to the orders 3 and 4 and introduce the Rush-Larsen schemes of order k (shortly denoted RL\_k). The RL\_k schemes are explicit multistep exponential integrators. They display a simple general formulation and an easy implementation. The RL\_k schemes are shown to be stable under perturbation and convergent of order k. Their Dahlquist stability analysis is performed. They have a very large stability domain provided that the stabilizer associated with the method captures well enough the stiff modes of the problem. The RL\_k method is numerically studied as applied to the membrane equation in cardiac electrophysiology. The RL k schemes are shown to be stable under perturbation and convergent oforder k. Their Dahlquist stability analysis is performed. They have a very large stability domain provided that the stabilizer associated with the method captures well enough the stiff modes of the problem. The RL k method is numerically studied as applied to the membrane equation in cardiac electrophysiology

High-order implicit palindromic discontinuous Galerkin method for kinetic-relaxation approximation

We construct a high order discontinuous Galerkin method for solving general hyperbolic systems of conservation laws. The method is CFL-less, matrix-free, has the complexity of an explicit scheme and can be of arbitrary order in space and time. The construction is based on: (a) the representation of the system of conservation laws by a kinetic vectorial representation with a stiff relaxation term; (b) a matrix-free, CFL-less implicit discontinuous Galerkin transport solver; and (c) a stiffly accurate composition method for time integration. The method is validated on several one-dimensional test cases. It is then applied on two-dimensional and three-dimensional test cases: flow past a cylinder, magnetohydrodynamics and multifluid sedimentation

On the convergence of Lawson methods for semilinear stiff problems

Since their introduction in 1967, Lawson methods have achieved constant interest in the time discretization of evolution equations. The methods were originally devised for the numerical solution of stiff differential equations. Meanwhile, they constitute a well-established class of exponential integrators. The popularity of Lawson methods is in some contrast to the fact that they may have a bad convergence behaviour, since they do not satisfy any of the stiff order conditions. The aim of this paper is to explain this discrepancy. It is shown that non-stiff order conditions together with appropriate regularity assumptions imply high-order convergence of Lawson methods. Note, however, that the term regularity here includes the behaviour of the solution at the boundary. For instance, Lawson methods will behave well in the case of periodic boundary conditions, but they will show a dramatic order reduction for, e.g., Dirichlet boundary conditions. The precise regularity assumptions required for high-order convergence are worked out in this paper and related to the corresponding assumptions for splitting schemes. In contrast to previous work, the analysis is based on expansions of the exact and the numerical solution along the flow of the homogeneous problem. Numerical examples for the Schr\"odinger equation are included

Emergent properties of the G1/S network

Tato práce se zabývá buněčným cyklem kvasinky Saccgaromyces cerevisiae. Oblastí našeho zájmu je přechod mezi G1 a S fází, kde je naším cílem identifikovat velikosti buňky v době počátku DNA replikace. Nejprve se věnujeme nedávno publikovanému matematickému modelu, který popisuje mechanismy vedoucí k S fázi. Práce poskytuje detailní popis tohoto modelu, stejně jako časový průběh některých důležitých proteinů či jejich sloučenin. Dále se zabýváme pravděpodobnostním modelem aktivace replikačních počátků DNA. Nově uvažujeme vliv šíření DNA replikace mezi sousedícími počátky a analyzujeme jeho důsledky. Poskytujeme také senzitivní analýzu kritické velikosti buňky vzhledem ke konstantám popisujícím dynamiku reakcí v modelu G1/S přechodu.In this thesis we deal with the cell cycle of the yeast Saccharomyces cerevisiae. We are interested in its G1 to S transition, and our main goal is to determine the cell size at the onset of its DNA replication. At first, we study a recent mathematical model describing the mechanisms leading to the S phase, we provide its detailed description and present the dynamics of some significant protein and protein complexes. Further, we take a closer look at the probabilistic model for firing of DNA replication origins. We newly consider the influence of DNA replication spreading among neighboring origins, and we analyze its consequences. We also provide a sensitivity analysis of the critical cell size with respect to rate constants of G1 to S transition model.