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.

A 5-Step Block Predictor and 4-Step Corrector Methods for Solving General Second Order Ordinary Differential Equations

A 5-step block predictor and 4-step corrector methods aimed at solving general second order ordinary differential equations directly will be constructed and implemented on non-stiff problems. This method, which extends the work of block predictor-corrector methods using variable step size technique possess some computational advantages of choosing a suitable step size, deciding the stopping criteria and error control. In addition, some selected theoretical properties of the method will be investigated as well as determination of the region of absolute stability. Numerical results will be given to show the efficiency of the new metho

Numerical Solution of Ordinary Differential Equations (ODES) from Reformulated block 3-step AdamsBashforth method

In this paper, efficient AdamsBashforth Runge-Kutta (ABRK) method are constructed.This is achieved by reformulating the block AdamsBashforth methods as a class of Runge-Kutta methods for 3-step.The reformulated methods are of orders 4 and their absolute stability regions construc ted are shown to be A-Stable.The newly constructed methods are tested on non stiff initial value problems and the solution reveals that the the methods are efficient

New gaussian points for the solution of first order ordinary differential equations

The Gauss Radau and the Lobatto points make use of the roots of the Legendre polynomial located within the step [-1,1]. In this paper, a new set of Gaussian points has been proposed and used as collocation points for the construction of block numerical methods for the solution of first order IVP through transformation within the step [Xn,Xn+2]. The new points resulted into stable numerical block methods of order 2m suitable for solving both stiff and non-stiff IVP. Numerical experiments carried out using the new Gaussian points revealed there efficiency on stiff differential equations. The results also reveal that methods using the new Gaussian points are more accurate than those using the standard Gaussian points on non-stiff initial value problems. Keywords: Gaussian points, Collocation points, Legendre polynomial, Gauss,Lobatto, Block integrators, stiff and non-stiff IVP’

Description and use of LSODE, the Livermore Solver for Ordinary Differential Equations

LSODE, the Livermore Solver for Ordinary Differential Equations, is a package of FORTRAN subroutines designed for the numerical solution of the initial value problem for a system of ordinary differential equations. It is particularly well suited for 'stiff' differential systems, for which the backward differentiation formula method of orders 1 to 5 is provided. The code includes the Adams-Moulton method of orders 1 to 12, so it can be used for nonstiff problems as well. In addition, the user can easily switch methods to increase computational efficiency for problems that change character. For both methods a variety of corrector iteration techniques is included in the code. Also, to minimize computational work, both the step size and method order are varied dynamically. This report presents complete descriptions of the code and integration methods, including their implementation. It also provides a detailed guide to the use of the code, as well as an illustrative example problem

Unconditional Stability for Multistep ImEx Schemes: Theory

This paper presents a new class of high order linear ImEx multistep schemes with large regions of unconditional stability. Unconditional stability is a desirable property of a time stepping scheme, as it allows the choice of time step solely based on accuracy considerations. Of particular interest are problems for which both the implicit and explicit parts of the ImEx splitting are stiff. Such splittings can arise, for example, in variable-coefficient problems, or the incompressible Navier-Stokes equations. To characterize the new ImEx schemes, an unconditional stability region is introduced, which plays a role analogous to that of the stability region in conventional multistep methods. Moreover, computable quantities (such as a numerical range) are provided that guarantee an unconditionally stable scheme for a proposed implicit-explicit matrix splitting. The new approach is illustrated with several examples. Coefficients of the new schemes up to fifth order are provided.Comment: 33 pages, 7 figure

A Class of A-Stable Order Four and Six Linear Multistep Methods for Stiff Initial Value Problems

A new three and five step block linear methods based on the Adams family for the direct solution of stiff initial value problems (IVPs) are proposed. The main methods together with the additional methods which constitute the block methods are derived via interpolation and collocation procedures. These methods are of uniform order four and six for the three and five step methods respectively. The stability analysis of the two methods indicates that the methods are A–stable, consistent and zero stable. Numerical results obtained using the proposed new block methods show that they are attractive for the solutions of stiff problems and compete favorably with the well-known Matlab stiff ODE solver ODE23S. Keywords: Linear multistep methods, initial value problems, interpolation and collocation